Compositions for the treatment of skin conditions

ABSTRACT

Described herein are methods and compositions for the treatment of skin conditions associated the dysbiosis. Further described herein is the use of metabolites for treatment of dysregulated microbiota in a subject. Such metabolites can be produced by microorganisms present in a higher abundance in the skin of healthy subjects as compared to the skin of a subject having dysbiosis of the skin. In addition, compositions and methods provided herein describe the use of metabolites as part of a combination therapy.

This application is a continuation of U.S. patent application Ser. No.16/401,986, filed May 2, 2019, which claims benefit of U.S. ProvisionalApplication No. 62/670,341, filed on May 11, 2018, and U.S. ProvisionalApplication No. 62/703,737, filed on Jul. 26, 2018, both of which areincorporated herein by reference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII Format via EFS-Web and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Apr. 22, 2019, isnamed 53654-704 301 SL.txt and is 2,122 bytes in size.

BACKGROUND

Dysbiosis of the skin microbiome is associated with a variety ofdiseases where the skin barrier is disrupted and inflammation at thesite of disruption may be increased as well. For example, in the case ofatopic dermatitis, the skin microbiome of healthy subjects issignificantly different from that of atopic dermatitis subjects.Symptoms of atopic dermatitis are often attributed to loss of commensaldiversity. Microbiota dysfunction is also a feature of atopic dermatitispathology. Overgrowth and infection of Staphylococcus aureus arecontributors and consequences of immune imbalance and poor barrierfunction. Antibiotic treatments that mitigate growth of S. aureus canimprove atopic dermatitis symptoms, but often cannot normalize theunderlying pathology. Thus, there is a need for improved therapies fortreatment of skin diseases associated with dysbiosis.

BRIEF SUMMARY

Provided herein are pharmaceutical compositions comprising: ametabolite, wherein the metabolite is present in an amount sufficient toreduce skin dysbiosis in a subject in need thereof, and wherein themetabolite is produced from a species of gram-negative bacteria that ismore highly abundant in skin from a subject that does not have skindysbiosis as compared to abundance of the species in skin from a subjecthaving skin dysbiosis; and a pharmaceutically-acceptable carrier.Further provided herein are compositions, wherein the species ofgram-negative bacteria comprises a Roseomonas genus bacterium. Furtherprovided herein are compositions, wherein the Roseomonas genus bacteriumis Roseomonas mucosa. Further provided herein are compositions, whereinthe species of gram-negative bacteria comprises a Pseudomonas genusbacterium. Further provided herein are compositions, wherein thePseudomonas genus bacterium is Pseudomonas aeruginosa, Pseudomonasluteola, or Pseudomonas oryzihabitans. Further provided herein arecompositions, wherein the subject has atopic dermatitis, rosacea, orpsoriasis. Further provided herein are compositions, wherein themetabolite is N4-acetylaminobutanal, 5-ethylpentadecane-2,4-dione,ricinoleic acid methyl ester, trenbolone acetate, orN-(2-hydroxyethyl)-11(12)-epoxy-5Z,8Z,14Z-eicosatrienamide. Furtherprovided herein are compositions, wherein the metabolite is a lipid.Further provided herein are compositions, wherein the lipid comprisesphosphatidylethanolamine 36:2, phosphatidylcholine 37:0,phosphatidylcholine 37:2, phosphatidylcholine 38:2,phosphatidylcholine(18:2(9Z,12Z)/18:0), phosphatidylethanolamine14:0/20:1, phosphatidylethanolamine 22:1/14:1, phosphatidylethanolamine36:2, or 8-keto palmitic acid. Further provided herein are compositions,wherein the metabolite is a peptide. Further provided herein arecompositions, wherein the peptide comprises Tyr-Leu-Arg. Furtherprovided herein are compositions, wherein the metabolite is a sugar.Further provided herein are compositions, wherein the sugar comprisesmaltopentaose. Further provided herein are compositions, wherein themetabolite is a nucleotide. Further provided herein are compositions,wherein the nucleotide comprises 2′-deoxyguanosine 5′-monophosphate.Further provided herein are compositions, comprising a plurality ofdifferent metabolites produced from the same or different species ofgram-negative bacteria that are more highly abundant in skin from thesubject that does not have atopic dermatitis as compared to abundance ofthe species in skin from the subject having atopic dermatitis. Furtherprovided herein are compositions, wherein the composition is in atopical, rectal, or oral dosage form. Further provided herein arecompositions, wherein the topical dosage form is a liquid, cream, gel,or foam. Provided herein are methods for treatment of skin dysbiosis,comprising: administering to a subject in need thereof a pharmaceuticalcomposition provided herein. Further provided herein are methods,wherein the pharmaceutical composition is topically, orally, or rectallyadministered. Further provided herein are methods, wherein thepharmaceutical composition is topically administered by spraying.Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject at least two times per aweek. Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject every other day over a week.Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject once a day. Further providedherein are methods, wherein the subject is an adult. Further providedherein are methods, wherein the subject is a child. Further providedherein are methods, wherein the subject is an infant. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa bacterium comprises a nucleic acid sequence of SEQID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa comprises a nucleic acid sequence of SEQ ID NO: 1, SEQID NO: 2, and SEQ ID NO: 3. Further provide herein are pharmaceuticalcompositions wherein the at least one strain of Roseomonas mucosacomprises isolate RM-A, RM-B or RM-C. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa is isolate RM-A, RM-B or RM-C. Further provide hereinare pharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa consists of isolates RM-A, RM-B and RM-C.

Provided herein are pharmaceutical compositions comprising: ametabolite, wherein the metabolite is present in an amount sufficient toreduce atopic dermatitis in a subject in need thereof, and wherein themetabolite is produced from a species of gram-negative bacteria that ismore highly abundant in skin from a subject that does not have atopicdermatitis as compared to abundance of the species in skin from asubject having atopic dermatitis; and a pharmaceutically-acceptablecarrier. Further provided herein are compositions, wherein the speciesof gram-negative bacteria comprises a Roseomonas genus bacterium.Further provided herein are compositions, wherein the Roseomonas genusbacterium is Roseomonas mucosa. Further provided herein arecompositions, wherein the species of gram-negative bacteria comprises aPseudomonas genus bacterium. Further provided herein are compositions,wherein the Pseudomonas genus bacterium is Pseudomonas aeruginosa,Pseudomonas luteola, or Pseudomonas oryzihabitans. Further providedherein are compositions, wherein the metabolite isN4-acetylaminobutanal, 5-ethylpentadecane-2,4-dione, ricinoleic acidmethyl ester, trenbolone acetate, orN-(2-hydroxyethyl)-11(12)-epoxy-5Z,8Z,14Z-eicosatrienamide. Furtherprovided herein are compositions, wherein the metabolite is a lipid.Further provided herein are compositions, wherein the lipid comprisesphosphatidylethanolamine 36:2, phosphatidylcholine 37:0,phosphatidylcholine 37:2, phosphatidylcholine 38:2,phosphatidylcholine(18:2(9Z,12Z)/18:0), phosphatidylethanolamine14:0/20:1, phosphatidylethanolamine 22:1/14:1, phosphatidylethanolamine36:2, or 8-keto palmitic acid. Further provided herein are compositions,wherein the metabolite is a peptide. Further provided herein arecompositions, wherein the peptide comprises Tyr-Leu-Arg. Furtherprovided herein are compositions, wherein the metabolite is a sugar.Further provided herein are compositions, wherein the sugar comprisesmaltopentaose. Further provided herein are compositions, wherein themetabolite is a nucleotide. Further provided herein are compositions,wherein the nucleotide comprises 2′-deoxyguanosine 5′-monophosphate.Further provided herein are compositions, comprising a plurality ofdifferent metabolites produced from the same or different species ofgram-negative bacteria that are more highly abundant in skin from thesubject that does not have atopic dermatitis as compared to abundance ofthe species in skin from the subject having atopic dermatitis. Furtherprovided herein are compositions, wherein the composition is in atopical, rectal, or oral dosage form. Further provided herein arecompositions, wherein the topical dosage form is a liquid, cream, gel,or foam. Provided herein are methods for treatment of atopic dermatitis,comprising: administering to a subject in need thereof a pharmaceuticalcomposition provided herein. Further provided herein are methods,wherein the pharmaceutical composition is topically, orally, or rectallyadministered. Further provided herein are methods, wherein thepharmaceutical composition is topically administered by spraying.Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject at least two times per aweek. Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject every other day over a week.Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject once a day. Further providedherein are methods, wherein the subject is an adult. Further providedherein are methods, wherein the subject is a child. Further providedherein are methods, wherein the subject is an infant. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa bacterium comprises a nucleic acid sequence of SEQID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa comprises a nucleic acid sequence of SEQ ID NO: 1, SEQID NO: 2, and SEQ ID NO: 3. Further provide herein are pharmaceuticalcompositions wherein the at least one strain of Roseomonas mucosacomprises isolate RM-A, RM-B or RM-C. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa is isolate RM-A, RM-B or RM-C. Further provide hereinare pharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa consists of isolates RM-A, RM-B and RM-C.

Provided herein are pharmaceutical compositions comprising: a firsttherapeutic agent, wherein the first therapeutic agent is a metabolite,wherein the metabolite is produced from a species of gram-negativebacteria that is more highly abundant in skin from a subject that doesnot have skin dysbiosis as compared to abundance of the species in skinfrom a subject having skin dysbiosis; and a second therapeutic agent,wherein the first therapeutic agent is present in an amount to enhancethe second therapeutic agent in treatment of skin dysbiosis. Furtherprovided herein are compositions, wherein the species of gram-negativebacteria comprises a Roseomonas genus bacterium. Further provided hereinare compositions, wherein the Roseomonas genus bacterium is Roseomonasmucosa. Further provided herein are compositions, wherein the species ofgram-negative bacteria comprises a Pseudomonas genus bacterium. Furtherprovided herein are compositions, wherein the Pseudomonas genusbacterium is Pseudomonas aeruginosa, Pseudomonas luteola, or Pseudomonasoryzihabitans. Further provided herein are compositions, wherein thesubject has atopic dermatitis, rosacea, or psoriasis. Further providedherein are compositions, wherein the metabolite isN4-acetylaminobutanal, 5-ethylpentadecane-2,4-dione, ricinoleic acidmethyl ester, trenbolone acetate, orN-(2-hydroxyethyl)-11(12)-epoxy-5Z,8Z,14Z-eicosatrienamide. Furtherprovided herein are compositions, wherein the metabolite is a lipid.Further provided herein are compositions, wherein the lipid comprisesphosphatidylethanolamine 36:2, phosphatidylcholine 37:0,phosphatidylcholine 37:2, phosphatidylcholine 38:2,phosphatidylcholine(18:2(9Z,12Z)/18:0), phosphatidylethanolamine14:0/20:1, phosphatidylethanolamine 22:1/14:1, phosphatidylethanolamine36:2, or 8-keto palmitic acid. Further provided herein are compositions,wherein the metabolite is a peptide. Further provided herein arecompositions, wherein the peptide comprises Tyr-Leu-Arg. Furtherprovided herein are compositions, wherein the metabolite is a sugar.Further provided herein are compositions, wherein the sugar comprisesmaltopentaose. Further provided herein are compositions, wherein themetabolite is a nucleotide. Further provided herein are compositions,wherein the nucleotide comprises 2′-deoxyguanosine 5′-monophosphate.Further provided herein are compositions, comprising a plurality ofdifferent metabolites produced from the same or different species ofgram-negative bacteria that are more highly abundant in skin from thesubject that does not have atopic dermatitis as compared to abundance ofthe species in skin from the subject having atopic dermatitis. Furtherprovided herein are compositions, wherein the second therapeutic agentis a microorganism, calcineurin inhibitor, antibody, small molecule, orsteroid. Further provided herein are compositions, wherein themicroorganism is a species of gram-negative bacteria. Further providedherein are compositions, wherein the species of gram-negative bacteriacomprises a Roseomonas genus bacterium. Further provided herein arecompositions, wherein the Roseomonas genus bacterium is Roseomonasmucosa. Further provided herein are compositions, wherein the species ofgram-negative bacteria comprises a Pseudomonas genus bacterium. Furtherprovided herein are compositions, wherein the Pseudomonas genusbacterium is Pseudomonas aeruginosa, Pseudomonas luteola, or Pseudomonasoryzihabitans. Further provided herein are compositions, wherein thegram-negative bacteria are present in an amount of from 10³ to 10¹²colony forming units. Further provided herein are compositions, whereinthe composition is in a topical, rectal, or oral dosage form. Furtherprovided herein are compositions, wherein the topical dosage form is aliquid, cream, gel, or foam. Provided herein are methods for treatmentof skin dysbiosis, comprising: administering to a subject in needthereof a pharmaceutical composition provided herein. Further providedherein are methods, wherein the pharmaceutical composition is topically,orally, or rectally administered. Further provided herein are methods,wherein the pharmaceutical composition is topically administered byspraying. Further provided herein are methods, wherein thepharmaceutical composition is administered to the subject at least twotimes per a week. Further provided herein are methods, wherein thepharmaceutical composition is administered to the subject every otherday over a week. Further provided herein are methods, wherein thepharmaceutical composition is administered to the subject once a day.Further provided herein are methods, wherein the subject is an adult.Further provided herein are methods, wherein the subject is a child.Further provided herein are methods, wherein the subject is an infant.Further provide herein are pharmaceutical compositions wherein the atleast one strain of Roseomonas mucosa bacterium comprises a nucleic acidsequence of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa comprises a nucleic acid sequence of SEQ ID NO: 1,SEQ ID NO: 2, and SEQ ID NO: 3. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa comprises isolate RM-A, RM-B or RM-C. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa is isolate RM-A, RM-B or RM-C. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa consists of isolates RM-A, RM-B and RM-C.

Provided herein are pharmaceutical compositions comprising: a firsttherapeutic agent, wherein the first therapeutic agent is a metabolite,wherein the metabolite is produced from a species of gram-negativebacteria that is more highly abundant in skin from a subject that doesnot have atopic dermatitis as compared to abundance of the species inskin from a subject having atopic dermatitis; and a second therapeuticagent, wherein the first therapeutic agent is present in an amount toenhance the second therapeutic agent in treatment of atopic dermatitis.Further provided herein are compositions, wherein the species ofgram-negative bacteria comprises a Roseomonas genus bacterium. Furtherprovided herein are compositions, wherein the Roseomonas genus bacteriumis Roseomonas mucosa. Further provided herein are compositions, whereinthe species of gram-negative bacteria comprises a Pseudomonas genusbacterium. Further provided herein are compositions, wherein thePseudomonas genus bacterium is Pseudomonas aeruginosa, Pseudomonasluteola, or Pseudomonas oryzihabitans. Further provided herein arecompositions, wherein the metabolite is N4-acetylaminobutanal,5-ethylpentadecane-2,4-dione, ricinoleic acid methyl ester, trenboloneacetate, or N-(2-hydroxyethyl)-11(12)-epoxy-5Z,8Z,14Z-eicosatrienamide.Further provided herein are compositions, wherein the metabolite is alipid. Further provided herein are compositions, wherein the lipidcomprises phosphatidylethanolamine 36:2, phosphatidylcholine 37:0,phosphatidylcholine 37:2, phosphatidylcholine 38:2,phosphatidylcholine(18:2(9Z,12Z)/18:0), phosphatidylethanolamine14:0/20:1, phosphatidylethanolamine 22:1/14:1, phosphatidylethanolamine36:2, or 8-keto palmitic acid. Further provided herein are compositions,wherein the metabolite is a peptide. Further provided herein arecompositions, wherein the peptide comprises Tyr-Leu-Arg. Furtherprovided herein are compositions, wherein the metabolite is a sugar.Further provided herein are compositions, wherein the sugar comprisesmaltopentaose. Further provided herein are compositions, wherein themetabolite is a nucleotide. Further provided herein are compositions,wherein the nucleotide comprises 2′-deoxyguanosine 5′-monophosphate.Further provided herein are compositions, comprising a plurality ofdifferent metabolites produced from the same or different species ofgram-negative bacteria that are more highly abundant in skin from thesubject that does not have atopic dermatitis as compared to abundance ofthe species in skin from the subject having atopic dermatitis. Furtherprovided herein are compositions, wherein the second therapeutic agentis a microorganism, calcineurin inhibitor, antibody, small molecule, orsteroid. Further provided herein are compositions, wherein themicroorganism is a species of gram-negative bacteria. Further providedherein are compositions, wherein the species of gram-negative bacteriacomprises a Roseomonas genus bacterium. Further provided herein arecompositions, wherein the Roseomonas genus bacterium is Roseomonasmucosa. Further provided herein are compositions, wherein the species ofgram-negative bacteria comprises a Pseudomonas genus bacterium. Furtherprovided herein are compositions, wherein the Pseudomonas genusbacterium is Pseudomonas aeruginosa, Pseudomonas luteola, or Pseudomonasoryzihabitans. Further provided herein are compositions, wherein thegram-negative bacteria are present in an amount of from 10³ to 10¹²colony forming units. Further provided herein are compositions, whereinthe composition is in a topical, rectal, or oral dosage form. Furtherprovided herein are compositions, wherein the topical dosage form is aliquid, cream, gel, or foam. Provided herein are methods for treatmentof atopic dermatitis, comprising: administering to a subject in needthereof a pharmaceutical composition provided herein. Further providedherein are methods, wherein the pharmaceutical composition is topically,orally, or rectally administered. Further provided herein are methods,wherein the pharmaceutical composition is topically administered byspraying. Further provided herein are methods, wherein thepharmaceutical composition is administered to the subject at least twotimes per a week. Further provided herein are methods, wherein thepharmaceutical composition is administered to the subject every otherday over a week. Further provided herein are methods, wherein thepharmaceutical composition is administered to the subject once a day.Further provided herein are methods, wherein the subject is an adult.Further provided herein are methods, wherein the subject is a child.Further provided herein are methods, wherein the subject is an infant.Further provide herein are pharmaceutical compositions wherein the atleast one strain of Roseomonas mucosa bacterium comprises a nucleic acidsequence of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa comprises a nucleic acid sequence of SEQ ID NO: 1,SEQ ID NO: 2, and SEQ ID NO: 3. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa comprises isolate RM-A, RM-B or RM-C. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa is isolate RM-A, RM-B or RM-C. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa consists of isolates RM-A, RM-B and RM-C.

Provided herein are pharmaceutical compositions comprising: ametabolite, wherein the metabolite is present in an amount sufficient toreduce skin dysbiosis in a subject in need thereof, and wherein themetabolite is produced from a species of Roseomonas or a species ofPseudomonas that is more highly abundant in skin from a subject thatdoes not have skin dysbiosis as compared to abundance of the species inskin from a subject having skin dysbiosis; and a second therapeuticagent, wherein the first therapeutic agent is present in an amount toenhance the second therapeutic agent in treatment of skin dysbiosis.Further provided herein are compositions, wherein the species ofRoseomonas is Roseomonas mucosa. Further provided herein arecompositions, wherein the species of Pseudomonas is Pseudomonasaeruginosa, Pseudomonas luteola, or Pseudomonas oryzihabitans. Furtherprovided herein are compositions, wherein the subject has atopicdermatitis, rosacea, or psoriasis. Further provided herein arecompositions, wherein the metabolite is N4-acetylaminobutanal,5-ethylpentadecane-2,4-dione, ricinoleic acid methyl ester, trenboloneacetate, or N-(2-hydroxyethyl)-11(12)-epoxy-5Z,8Z,14Z-eicosatrienamide.Further provided herein are compositions, wherein the metabolite is alipid. Further provided herein are compositions, wherein the lipidcomprises phosphatidylethanolamine 36:2, phosphatidylcholine 37:0,phosphatidylcholine 37:2, phosphatidylcholine 38:2,phosphatidylcholine(18:2(9Z,12Z)/18:0), phosphatidylethanolamine14:0/20:1, phosphatidylethanolamine 22:1/14:1, phosphatidylethanolamine36:2, or 8-keto palmitic acid. Further provided herein are compositions,wherein the metabolite is a peptide. Further provided herein arecompositions, wherein the peptide comprises Tyr-Leu-Arg. Furtherprovided herein are compositions, wherein the metabolite is a sugar.Further provided herein are compositions, wherein the sugar comprisesmaltopentaose. Further provided herein are compositions, wherein themetabolite is a nucleotide. Further provided herein are compositions,wherein the nucleotide comprises 2′-deoxyguanosine 5′-monophosphate.Further provided herein are compositions, wherein the second therapeuticagent is a wherein the second therapeutic agent is a microorganism,calcineurin inhibitor, antibody, small molecule, or steroid. Furtherprovided herein are compositions, wherein the microorganism is agram-negative bacteria. Further provided herein are compositions,wherein the gram-negative bacteria comprise a Roseomonas genusbacterium. Further provided herein are compositions, wherein theRoseomonas genus bacterium is Roseomonas mucosa. Further provided hereinare compositions, wherein the species of gram-negative bacteriacomprises a Pseudomonas genus bacterium. Further provided herein arecompositions, wherein the Pseudomonas genus bacterium is Pseudomonasaeruginosa, Pseudomonas luteola, or Pseudomonas oryzihabitans. Furtherprovided herein are compositions, wherein the gram-negative bacteria arepresent in an amount of from 10³ to 10¹² colony forming units. Furtherprovided herein are compositions, wherein the composition is in atopical, rectal, or oral dosage form. Further provided herein arecompositions, wherein the topical dosage form is a liquid, cream, gel,or foam. Provided herein are methods for treatment of skin dysbiosis,comprising: administering to a subject in need thereof a pharmaceuticalcomposition provided herein. Further provided herein are methods,wherein the subject has atopic dermatitis, rosacea, or psoriasis.Further provided herein are methods, wherein the pharmaceuticalcomposition is topically, orally, or rectally administered. Furtherprovided herein are methods, wherein the pharmaceutical composition istopically administered by spraying. Further provided herein are methods,wherein the pharmaceutical composition is administered to the subject atleast two times per a week. Further provided herein are methods, whereinthe pharmaceutical composition is administered to the subject everyother day over a week. Further provided herein are methods, wherein thepharmaceutical composition is administered to the subject once a day.Further provided herein are methods, wherein the subject is an adult.Further provided herein are methods, wherein the subject is a child.Further provided herein are methods, wherein the subject is an infant.Further provide herein are pharmaceutical compositions wherein the atleast one strain of Roseomonas mucosa bacterium comprises a nucleic acidsequence of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa comprises a nucleic acid sequence of SEQ ID NO: 1,SEQ ID NO: 2, and SEQ ID NO: 3. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa comprises isolate RM-A, RM-B or RM-C. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa is isolate RM-A, RM-B or RM-C. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa consists of isolates RM-A, RM-B and RM-C.

Provided herein are pharmaceutical compositions comprising: ametabolite, wherein the metabolite is present in an amount sufficient toreduce atopic dermatitis in a subject in need thereof, and wherein themetabolite is produced from a species of Roseomonas or a species ofPseudomonas that is more highly abundant in skin from a subject thatdoes not have atopic dermatitis as compared to abundance of the speciesin skin from a subject having atopic dermatitis; and a secondtherapeutic agent, wherein the first therapeutic agent is present in anamount to enhance the second therapeutic agent in treatment of skindysbiosis. Further provided herein are compositions, wherein the speciesof Roseomonas is Roseomonas mucosa. Further provided herein arecompositions, wherein the species of Pseudomonas is Pseudomonasaeruginosa, Pseudomonas luteola, or Pseudomonas oryzihabitans. Furtherprovided herein are compositions, wherein the metabolite isN4-acetylaminobutanal, 5-ethylpentadecane-2,4-dione, ricinoleic acidmethyl ester, trenbolone acetate, orN-(2-hydroxyethyl)-11(12)-epoxy-5Z,8Z,14Z-eicosatrienamide. Furtherprovided herein are compositions, wherein the metabolite is a lipid.Further provided herein are compositions, wherein the lipid comprisesphosphatidylethanolamine 36:2, phosphatidylcholine 37:0,phosphatidylcholine 37:2, phosphatidylcholine 38:2,phosphatidylcholine(18:2(9Z,12Z)/18:0), phosphatidylethanolamine14:0/20:1, phosphatidylethanolamine 22:1/14:1, phosphatidylethanolamine36:2, or 8-keto palmitic acid. Further provided herein are compositions,wherein the metabolite is a peptide. Further provided herein arecompositions, wherein the peptide comprises Tyr-Leu-Arg. Furtherprovided herein are compositions, wherein the metabolite is a sugar.Further provided herein are compositions, wherein the sugar comprisesmaltopentaose. Further provided herein are compositions, wherein themetabolite is a nucleotide. Further provided herein are compositions,wherein the nucleotide comprises 2′-deoxyguanosine 5′-monophosphate.Further provided herein are compositions, wherein the second therapeuticagent is a wherein the second therapeutic agent is a microorganism,calcineurin inhibitor, antibody, small molecule, or steroid. Furtherprovided herein are compositions, wherein the microorganism is agram-negative bacteria. Further provided herein are compositions,wherein the gram-negative bacteria comprise a Roseomonas genusbacterium. Further provided herein are compositions, wherein theRoseomonas genus bacterium is Roseomonas mucosa. Further provided hereinare compositions, wherein the species of gram-negative bacteriacomprises a Pseudomonas genus bacterium. Further provided herein arecompositions, wherein the Pseudomonas genus bacterium is Pseudomonasaeruginosa, Pseudomonas luteola, or Pseudomonas oryzihabitans. Furtherprovided herein are compositions, wherein the gram-negative bacteria arepresent in an amount of from 10³ to 10¹² colony forming units. Furtherprovided herein are compositions, wherein the composition is in atopical, rectal, or oral dosage form. Further provided herein arecompositions, wherein the topical dosage form is a liquid, cream, gel,or foam. Provided herein are methods for treatment of atopic dermatitis,comprising: administering to a subject in need thereof a pharmaceuticalcomposition provided herein. Further provided herein are methods,wherein the pharmaceutical composition is topically, orally, or rectallyadministered. Further provided herein are methods, wherein thepharmaceutical composition is topically administered by spraying.Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject at least two times per aweek. Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject every other day over a week.Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject once a day. Further providedherein are methods, wherein the subject is an adult. Further providedherein are methods, wherein the subject is a child. Further providedherein are methods, wherein the subject is an infant. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa bacterium comprises a nucleic acid sequence of SEQID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa comprises a nucleic acid sequence of SEQ ID NO: 1, SEQID NO: 2, and SEQ ID NO: 3. Further provide herein are pharmaceuticalcompositions wherein the at least one strain of Roseomonas mucosacomprises isolate RM-A, RM-B or RM-C. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa is isolate RM-A, RM-B or RM-C. Further provide hereinare pharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa consists of isolates RM-A, RM-B and RM-C.

Provided herein are pharmaceutical compositions comprising: a firsttherapeutic agent, wherein the first therapeutic agent is a metabolite,wherein the metabolite is produced from a species of Roseomonas or aspecies of Pseudomonas that is more highly abundant in skin from asubject that does not have skin dysbiosis as compared to abundance ofthe species in skin from a subject having skin dysbiosis; and a secondtherapeutic agent, wherein the first therapeutic agent is present in anamount to enhance the second therapeutic agent in treatment of skindysbiosis. Further provided herein are compositions, wherein the speciesof Roseomonas is Roseomonas mucosa. Further provided herein arecompositions, wherein the species of Pseudomonas is Pseudomonasaeruginosa, Pseudomonas luteola, or Pseudomonas oryzihabitans. Furtherprovided herein are methods, wherein the subject has atopic dermatitis,rosacea, or psoriasis. Further provided herein are compositions, whereinthe metabolite is N4-acetylaminobutanal, 5-ethylpentadecane-2,4-dione,ricinoleic acid methyl ester, trenbolone acetate, orN-(2-hydroxyethyl)-11(12)-epoxy-5Z,8Z,14Z-eicosatrienamide. Furtherprovided herein are compositions, wherein the metabolite is a lipid.Further provided herein are compositions, wherein the lipid comprisesphosphatidylethanolamine 36:2, phosphatidylcholine 37:0,phosphatidylcholine 37:2, phosphatidylcholine 38:2,phosphatidylcholine(18:2(9Z,12Z)/18:0), phosphatidylethanolamine14:0/20:1, phosphatidylethanolamine 22:1/14:1, phosphatidylethanolamine36:2, or 8-keto palmitic acid. Further provided herein are compositions,wherein the metabolite is a peptide. Further provided herein arecompositions, wherein the peptide comprises Tyr-Leu-Arg. Furtherprovided herein are compositions, wherein the metabolite is a sugar.Further provided herein are compositions, wherein the sugar comprisesmaltopentaose. Further provided herein are compositions, wherein themetabolite is a nucleotide. Further provided herein are compositions,wherein the nucleotide comprises 2′-deoxyguanosine 5′-monophosphate.Further provided herein are compositions, wherein the second therapeuticagent is a wherein the second therapeutic agent is a microorganism,calcineurin inhibitor, antibody, small molecule, or steroid. Furtherprovided herein are compositions, wherein the microorganism is agram-negative bacteria. Further provided herein are compositions,wherein the gram-negative bacteria comprise a Roseomonas genusbacterium. Further provided herein are compositions, wherein theRoseomonas genus bacterium is Roseomonas mucosa. Further provided hereinare compositions, wherein the species of gram-negative bacteriacomprises a Pseudomonas genus bacterium. Further provided herein arecompositions, wherein the Pseudomonas genus bacterium is Pseudomonasaeruginosa, Pseudomonas luteola, or Pseudomonas oryzihabitans. Furtherprovided herein are compositions, wherein the gram-negative bacteria arepresent in an amount of from 10³ to 10¹² colony forming units. Furtherprovided herein are compositions, wherein the composition is in atopical, rectal, or oral dosage form. Further provided herein arecompositions, wherein the topical dosage form is a liquid, cream, gel,or foam. Provided herein are methods for treatment of atopic dermatitis,comprising: administering to a subject in need thereof a pharmaceuticalcomposition provided herein. Further provided herein are methods,wherein the pharmaceutical composition is topically, orally, or rectallyadministered. Further provided herein are methods, wherein thepharmaceutical composition is topically administered by spraying.Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject at least two times per aweek. Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject every other day over a week.Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject once a day. Further providedherein are methods, wherein the subject is an adult. Further providedherein are methods, wherein the subject is a child. Further providedherein are methods, wherein the subject is an infant. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa bacterium comprises a nucleic acid sequence of SEQID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa comprises a nucleic acid sequence of SEQ ID NO: 1, SEQID NO: 2, and SEQ ID NO: 3. Further provide herein are pharmaceuticalcompositions wherein the at least one strain of Roseomonas mucosacomprises isolate RM-A, RM-B or RM-C. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa is isolate RM-A, RM-B or RM-C. Further provide hereinare pharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa consists of isolates RM-A, RM-B and RM-C.

Provided herein are pharmaceutical compositions comprising: a firsttherapeutic agent, wherein the first therapeutic agent is a metabolite,wherein the metabolite is produced from a species of Roseomonas or aspecies of Pseudomonas that is more highly abundant in skin from asubject that does not have atopic dermatitis as compared to abundance ofthe species in skin from a subject having atopic dermatitis; and asecond therapeutic agent, wherein the first therapeutic agent is presentin an amount to enhance the second therapeutic agent in treatment ofatopic dermatitis. Further provided herein are compositions, wherein thespecies of Roseomonas is Roseomonas mucosa. Further provided herein arecompositions, wherein the species of Pseudomonas is Pseudomonasaeruginosa, Pseudomonas luteola, or Pseudomonas oryzihabitans. Furtherprovided herein are compositions, wherein the metabolite isN4-acetylaminobutanal, 5-ethylpentadecane-2,4-dione, ricinoleic acidmethyl ester, trenbolone acetate, orN-(2-hydroxyethyl)-11(12)-epoxy-5Z,8Z,14Z-eicosatrienamide. Furtherprovided herein are compositions, wherein the metabolite is a lipid.Further provided herein are compositions, wherein the lipid comprisesphosphatidylethanolamine 36:2, phosphatidylcholine 37:0,phosphatidylcholine 37:2, phosphatidylcholine 38:2,phosphatidylcholine(18:2(9Z,12Z)/18:0), phosphatidylethanolamine14:0/20:1, phosphatidylethanolamine 22:1/14:1, phosphatidylethanolamine36:2, or 8-keto palmitic acid. Further provided herein are compositions,wherein the metabolite is a peptide. Further provided herein arecompositions, wherein the peptide comprises Tyr-Leu-Arg. Furtherprovided herein are compositions, wherein the metabolite is a sugar.Further provided herein are compositions, wherein the sugar comprisesmaltopentaose. Further provided herein are compositions, wherein themetabolite is a nucleotide. Further provided herein are compositions,wherein the nucleotide comprises 2′-deoxyguanosine 5′-monophosphate.Further provided herein are compositions, wherein the second therapeuticagent is a wherein the second therapeutic agent is a microorganism,calcineurin inhibitor, antibody, small molecule, or steroid. Furtherprovided herein are compositions, wherein the microorganism is agram-negative bacteria. Further provided herein are compositions,wherein the gram-negative bacteria comprise a Roseomonas genusbacterium. Further provided herein are compositions, wherein theRoseomonas genus bacterium is Roseomonas mucosa. Further provided hereinare compositions, wherein the species of gram-negative bacteriacomprises a Pseudomonas genus bacterium. Further provided herein arecompositions, wherein the Pseudomonas genus bacterium is Pseudomonasaeruginosa, Pseudomonas luteola, or Pseudomonas oryzihabitans. Furtherprovided herein are compositions, wherein the gram-negative bacteria arepresent in an amount of from 10³ to 10¹² colony forming units. Furtherprovided herein are compositions, wherein the composition is in atopical, rectal, or oral dosage form. Further provided herein arecompositions, wherein the topical dosage form is a liquid, cream, gel,or foam. Provided herein are methods for treatment of atopic dermatitis,comprising: administering to a subject in need thereof a pharmaceuticalcomposition provided herein. Further provided herein are methods,wherein the pharmaceutical composition is topically, orally, or rectallyadministered. Further provided herein are methods, wherein thepharmaceutical composition is topically administered by spraying.Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject at least two times per aweek. Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject every other day over a week.Further provided herein are methods, wherein the pharmaceuticalcomposition is administered to the subject once a day. Further providedherein are methods, wherein the subject is an adult. Further providedherein are methods, wherein the subject is a child. Further providedherein are methods, wherein the subject is an infant. Further provideherein are pharmaceutical compositions wherein the at least one strainof Roseomonas mucosa bacterium comprises a nucleic acid sequence of SEQID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa comprises a nucleic acid sequence of SEQ ID NO: 1, SEQID NO: 2, and SEQ ID NO: 3. Further provide herein are pharmaceuticalcompositions wherein the at least one strain of Roseomonas mucosacomprises isolate RM-A, RM-B or RM-C. Further provide herein arepharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa is isolate RM-A, RM-B or RM-C. Further provide hereinare pharmaceutical compositions wherein the at least one strain ofRoseomonas mucosa consists of isolates RM-A, RM-B and RM-C.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A depicts a route of administration for bacteria via topicaladministration or oral administration, and for metabolites via topicaladministration.

FIG. 1B depicts a route of administration for bacteria via rectaladministration.

DETAILED DESCRIPTION

Provided herein are compositions and methods for treatment of acondition associated with skin dysbiosis by administering a metaboliteproduced by bacteria from a subject that does not have the conditionassociated with skin dysbiosis. The compositions and methods may furtherinclude an additional therapeutic agent for treatment of the conditionassociated with skin dysbiosis, where the presence of the metaboliteenhances the therapeutic effect of the additional therapeutic agent.Described herein are (1) microorganisms for treatment of skin conditionsassociated with dysbiosis; (2) metabolites for treatment of skinconditions associated with dysbiosis; (3) combination therapies; (4)therapeutic applications; (5) dosage forms; and (6) administrationschedules.

Provided herein are pharmaceutical compositions comprising: a metabolitewhich is more highly produced by bacteria from a subject that does nothave the condition associated with skin dysbiosis as compared toproduction of the metabolite by bacteria from a subject that has thecondition associated with skin dysbiosis; a mixture of live bacteria,wherein the mixture comprises: at least one strain of gram negativebacteria derived from a first donor that does not have a skin conditionassociated with dysbiosis; and, optionally, at least one strain of grampositive bacteria derived from a second donor that does not have theskin condition associated with dysbiosis, wherein the at least onestrain of gram negative bacteria and, optionally, the at least onestrain of gram positive bacteria are present in an amount sufficient fortreatment of the skin condition associated with dysbiosis in a subjectin need thereof, and wherein the pharmaceutical composition is in atopical dosage form. Further provided herein are compositions whereinthe pharmaceutical composition further comprises a pharmaceuticallyacceptable carrier. Further provided herein are compositions wherein theskin condition associated with dysbiosis is eczema, allergic eczema,flexural eczema, infantile eczema, nummular eczema, discoid lupus,prurigo Besnier, psoriasis, vitiligo, dermatitis, atopic dermatitis,perioral dermatitis, neurodermatitis, seborrheic dermatitis, rosacea, oracne. Further provided herein are compositions wherein the at least onestrain of gram negative bacteria is of the genus Pseudomonas, Pantoea,Moraxella, Roseomonas, or Vitreoscilla. Further provided herein arecompositions wherein the at least one strain of gram negative bacteriais Roseomonas mucosa, Pseudomonas aeruginosa, or Moraxella osloensis.Further provided herein are compositions wherein the at least one strainof gram negative bacteria is of the genus Staphylococci, Streptococci,Enterococci, Corynebacteriae, or Propionibacterii. Further providedherein are compositions wherein the at least one strain of gram positivebacteria is Staphylococcus epidermis, Staphylococcus cohnii, orStaphylococcus hominis. Provided herein are methods for treatment of askin condition associated with dysbiosis, comprising administering thepharmaceutical composition described herein to a subject in need thereoffor treatment of the skin condition associated with dysbiosis. Furtherprovided herein are methods wherein the skin condition associated withdysbiosis is eczema, allergic eczema, flexural eczema, infantile eczema,nummular eczema, discoid lupus, prurigo Besnier, psoriasis, vitiligo,dermatitis, atopic dermatitis, perioral dermatitis, neurodermatitis,seborrheic dermatitis, rosacea, or acne. Further provided herein aremethods wherein the pharmaceutical composition is administeredtopically. Further provided herein are methods wherein thepharmaceutical composition is administered to the subject at least twotimes per a week. Further provided herein are methods wherein thepharmaceutical composition is administered to the subject every otherday over a week. Further provided herein are methods wherein thepharmaceutical composition is administered to the subject once a day.Further provided herein are methods wherein the subject is an adult.Further provided herein are methods wherein the subject is a child.Further provided herein are methods wherein the subject is an infant.

Provided herein are methods for treatment of a skin condition associatedwith dysbiosis, comprising: providing a metabolite produced by bacteriafrom a subject that does not have the condition associated with skindysbiosis and at least one species of gram negative bacteria derivedfrom a donor that does not have a skin condition associated withdysbiosis; and topically administering the at least one species of gramnegative bacteria to a subject in need thereof, wherein the at least onespecies of gram negative bacteria is present in an amount sufficient fortreatment of a skin condition associated with dysbiosis, wherein theskin condition associated with dysbiosis is eczema, allergic eczema,flexural eczema, infantile eczema, nummular eczema, discoid lupus,prurigo Besnier, psoriasis, vitiligo, rosacea, or acne. Further providedherein are methods wherein the at least one species of gram negativebacteria provides for a relative increase in mRNA levels of defensin(β4A, CYP27b1, vitamin D receptor, cathelicidin, or filaggrin incultured human foreskin-derived primary keratinocytes within 24 hoursfollowing infection as compared to a same species type of gram negativebacteria from a subject having the skin condition associated withdysbiosis. Further provided herein are methods wherein the at least onespecies of gram negative bacteria provides for a relative increasereduction of Staphylococcus aureus growth within 24 hours afterco-infection in a mouse ear of the at least one species of gram negativebacteria with the a same species type of gram negative bacteria from asubject having the skin condition associated with dysbiosis. Furtherprovided herein are methods wherein the at least one species of gramnegative bacteria provides for a relative increase inlysophosphatidylcholine within 24 hours after co-infection in a mouseear of the at least one species of gram negative bacteria with a samespecies type of gram negative bacteria from a subject having the skincondition associated with dysbiosis. Further provided herein are methodswherein the at least one species of gram negative bacteria comprises atleast 2, 3, 4 or 5 different strains of gram negative bacteria. Furtherprovided herein are methods further comprising administering at least atleast one strain of gram positive bacteria derived from a donor thatdoes not have the skin condition associated with dysbiosis. In someinstances, the combination of therapeutic agents provides for atherapeutic effect that is enhanced compared to administration of anyone agent in the mixture alone. In some instances, a strain of grampositive bacteria is selected based on an increase relative abundancecompared the same species of bacteria in a subject suffering from a skincondition associated with dysbiosis. In some instances, the grampositive bacterial species is one or more species in the genus ofStaphylococci, Streptococci, Enterococci, Corynebacteriae, orPropionibacterii. In some instances, the Staphylococci species isStaphylococcus aureus, Staphylococcus hemolyticus, Staphylococcusauricularis, Staphylococcus warneri, Staphylococcus hominis,Staphylococcus epidermidis, Staphylococcus simulans, Staphylococcussciuri, Staphylococcus capitis, Staphylococcus saprophyticus,Staphylococcus xylosis, Staphylococcus cohnii, or Staphylococcus lentus.In some instances, the Streptococci species is Streptococcus bovis,Streptococcus agalactae, Streptococcus viridian, Streptococcuspneumonia, Streptococcus salivarius, or Streptococcus acidominimus. Insome instances, the Enterococci species is Enterococcus faecalis,Enterococcus Faecium, or Enterococcus gallinarium. In some instances,the Corynebacteriae species is Corynebacterium xerosis orCorynebacterium minutissimum. In some instances, the Propionibacteriumspecies is Propionibacterium acnes. In some instances, the gram-negativebacteria are a species of genera Pseudomonas, Pantoea, Moraxella,Roseomonas, Vitreoscilla, or Methylobacteria. In some instances theRoseomonas genus bacterium is Roseomonas aerilata, Roseomonas aerophila,Roseomonas aestuarii, Roseomonas alkaliterrae, Roseomonas aquatic,Roseomonas cervicalis, Roseomonas fauriae, Roseomonas frigidaquae,Roseomonas gilardii, Roseomonas lacus, Roseomonas ludipueritiae,Roseomonas mucosa, Roseomonas pecuniae, Roseomonas rhizosphaerae,Roseomonas riguiloci, Roseomonas rosea, Roseomonas soli, Roseomonasstagni, Roseomonas terrae, or Roseomonas vinacea. In some instances thePseudomonas genus bacterium is Pseudomonas aeruginosa, Pseudomonasluteola, or Pseudomonas oryzihabitans. In some instances the Pantoeagenus bacterium is Pantoea septica. In some instances the Moraxellagenus bacterium is Moraxella osloensis. In some instances theVitreoscilla genus bacterium is Vitreoscilla filiformis, Vitreoscillabeggiatoides, or Vitreoscilla beggiatoides.

Provided herein is are methods for treatment of a skin conditionassociated with dysbiosis, comprising: providing a metabolite which ismore highly produced by bacteria from a subject that does not have thecondition associated with skin dysbiosis as compared to production ofthe metabolite by bacteria from a subject that has the conditionassociated with skin dysbiosis and at least one species of gram negativebacteria derived from a first donor that does not have dermatitis;providing at least one species of gram positive bacteria derived from asecond donor that does not have dermatitis; and topically administeringthe at least one species of gram negative bacteria and the at least onespecies of gram positive bacteria to a subject in need thereof, whereinthe at least one species of gram negative bacteria and the at least onespecies of gram positive bacteria are present in an amount sufficientfor treatment of a skin condition associated with dysbiosis, wherein theskin condition associated with dysbiosis is dermatitis. Further providedherein are methods wherein the dermatitis is atopic dermatitis, perioraldermatitis, neurodermatitis, or seborrheic dermatitis. Further providedherein are methods wherein the at least one species of gram negativebacteria provides for a relative increase in mRNA levels of defensin(β4A, CYP27b1, vitamin D receptor, cathelicidin, or filaggrin incultured human foreskin-derived primary keratinocytes within 24 hoursfollowing infection as compared to a same species type of gram negativebacteria from a subject having the skin condition associated withdysbiosis. Further provided herein are methods wherein the at least onespecies of gram negative bacteria provides for a relative increasereduction of Staphylococcus aureus growth within 24 hours afterco-infection in a mouse ear of the at least one species of gram negativebacteria with the a same species type of gram negative bacteria from asubject having the skin condition associated with dysbiosis. Furtherprovided herein are methods wherein the at least one species of gramnegative bacteria provides for a relative increase inlysophosphatidylcholine within 24 hours after co-infection in a mouseear of the at least one species of gram negative bacteria with a samespecies type of gram negative bacteria from a subject having the skincondition associated with dysbiosis. Further provided herein are methodswherein the at least one species of gram negative bacteria comprises atleast 2, 3, 4 or 5 different strains of gram negative bacteria. In someinstances, the combination of therapeutic agents provides for atherapeutic effect that is enhanced compared to administration of anyone agent in the mixture alone. In some instances, a strain of grampositive bacteria is selected based on an increase relative abundancecompared the same species of bacteria in a subject suffering from a skincondition associated with dysbiosis. In some instances, the grampositive bacterial species is one or more species in the genus ofStaphylococci, Streptococci, Enterococci, Corynebacteriae, orPropionibacterii. In some instances, the Staphylococci species isStaphylococcus aureus, Staphylococcus hemolyticus, Staphylococcusauricularis, Staphylococcus warneri, Staphylococcus hominis,Staphylococcus epidermidis, Staphylococcus simulans, Staphylococcussciuri, Staphylococcus capitis, Staphylococcus saprophyticus,Staphylococcus xylosis, Staphylococcus cohnii, or Staphylococcus lentus.In some instances, the Streptococci species is Streptococcus bovis,Streptococcus agalactae, Streptococcus viridian, Streptococcuspneumonia, Streptococcus salivarius, or Streptococcus acidominimus. Insome instances, the Enterococci species is Enterococcus faecalis,Enterococcus Faecium, or Enterococcus gallinarium. In some instances,the Corynebacteriae species is Corynebacterium xerosis orCorynebacterium minutissimum. In some instances, the Propionibacteriumspecies is Propionibacterium acnes. In some instances, the gram-negativebacteria are a species of genera Pseudomonas, Pantoea, Moraxella,Roseomonas, Vitreoscilla, or Methylobacteria. In some instances theRoseomonas genus bacterium is Roseomonas aerilata, Roseomonas aerophila,Roseomonas aestuarii, Roseomonas alkaliterrae, Roseomonas aquatic,Roseomonas cervicalis, Roseomonas fauriae, Roseomonas frigidaquae,Roseomonas gilardii, Roseomonas lacus, Roseomonas ludipueritiae,Roseomonas mucosa, Roseomonas pecuniae, Roseomonas rhizosphaerae,Roseomonas riguiloci, Roseomonas rosea, Roseomonas soli, Roseomonasstagni, Roseomonas terrae, or Roseomonas vinacea. In some instances thePseudomonas genus bacterium is Pseudomonas aeruginosa, Pseudomonasluteola, or Pseudomonas oryzihabitans. In some instances the Pantoeagenus bacterium is Pantoea septica. In some instances the Moraxellagenus bacterium is Moraxella osloensis. In some instances theVitreoscilla genus bacterium is Vitreoscilla filiformis, Vitreoscillabeggiatoides, or Vitreoscilla beggiatoides.

Throughout this disclosure, various embodiments are presented in a rangeformat. It should be understood that the description in range format ismerely for convenience and brevity and should not be construed as aninflexible limitation on the scope of any embodiments. Accordingly, thedescription of a range should be considered to have specificallydisclosed all the possible subranges as well as individual numericalvalues within that range to the tenth of the unit of the lower limitunless the context clearly dictates otherwise. For example, descriptionof a range such as from 1 to 6 should be considered to have specificallydisclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual valueswithin that range, for example, 1.1, 2, 2.3, 5, and 5.9. This appliesregardless of the breadth of the range. The upper and lower limits ofthese intervening ranges may independently be included in the smallerranges, and are also encompassed within the invention, subject to anyspecifically excluded limit in the stated range. Where the stated rangeincludes one or both of the limits, ranges excluding either or both ofthose included limits are also included, unless the context clearlydictates otherwise.

The terminology used herein is for the purpose of describing particularinstances only and is not intended to be limiting of any embodiment. Asused herein, the singular forms “a,” “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. As used herein, the term “and/or” includes any and allcombinations of one or more of the associated listed items.

Unless specifically stated or obvious from context, as used herein, theterm “about” in reference to a number or range of numbers is understoodto mean the stated number and numbers +/−10% thereof, or 10% below thelower listed limit and 10% above the higher listed limit for the valueslisted for a range.

Microorganisms for Treatment of Skin Conditions Associated withDysbiosis

Provided herein are compositions for use in treatment of a skincondition associated with dysbiosis. Such compositions may includeisolated and/or purified bacteria and combinations of bacteria fromintact human skin, or propagated from such bacteria. These bacteria canfunction as a healthy microbiota or promote growth of residentmicrobiome when administered to a subject with a skin conditionassociated with dysbiosis. The compositions provided may treat,alleviate, delay, or reduce the likelihood of the symptoms of thecondition associated with dysbiosis. Exemplary skin conditionsassociated with dysbiosis for treatment using compositions describedherein include, without limitation, eczema, allergic eczema, flexuraleczema, infantile eczema, nummular eczema, discoid lupus, prurigoBesnier, psoriasis, vitiligo, dermatitis, atopic dermatitis, perioraldermatitis, neurodermatitis, seborrheic dermatitis, rosacea, and acne.

Provided herein are compositions comprising bacteria isolated from adonor subject that does not have a skin condition associated withdysbiosis, e.g., atopic dermatitis. A subject that does not have skincondition associated with dysbiosis is a subject without any observedpathological skin condition. Moreover, the donor subject may not haveany pathological condition, for example, a pathological condition of theskin and/or any internal organ. The donor subject can beimmunocompetent. The bacteria may be isolated from the skin of the donorsubject directly, or propagated in vitro using techniques for culturingbacteria.

Provided herein are genera, species, strains, and combinations ofstrains or species, originally found within the human skin microbiota ofa donor subject without a skin disease associated with dysbiosis. Suchspecies/strains may be selected for their ability to significantlyreduce the rate of skin pathogen replication. These species/strainsprovide a safe and effective means for modulating growth, replication,and disease severity of bacterial pathogens. Moreover, the compositionsprovided herein exclude pathogenic bacteria. As such, bacteria describedherein for use in compositions may be non-pathogenic when administeredto the skin of the subject, for example, an immunocompetent subject.Where the bacteria do not cause infection when administered to intacthuman skin, no pathogenesis is expected to be observed followingtreatment. Bacteria obtained from a donor subject may be isolated fromthe skin of various parts of the donor subject's body, for example, theforearm, antecubital fossa, and neck.

Compositions described herein, when administered to a subject having askin condition associated with dysbiosis, reduce the growth rate of aspecific pathogen present in the subject, for example, S. aureus.Bacteria with the capacity to durably reduce S. aureus in the skin canbe identified using a methodology for estimating an Ecological ControlFactor (ECF) for constituents within the human microbiota. The ECF canbe determined by assessing the antagonistic activity of a givencommensal strain or combination of strains towards a given pathogenusing an in vitro assay, resulting in observed levels of ecologicalcontrol at various concentrations of the added commensal strains. TheECF for a commensal strain or combination of strains is similar to theminimal inhibitory concentration (MIC) assessment that is employed inthe assessment of antibiotics. The ECF can be used to assess and rankthe relative potencies of commensal strains and combinations of strainsby the ability to antagonize skin pathogens. The ECF of a commensalstrain or combination of 20 strains can be calculated by assessing theconcentration of that composition that can mediate a given percentage ofinhibition (e.g., at least 10%, at least 20%, at least 50%, at least70%, at least 75%, at least 80%, at least 85%, at least 90%, at least95%, or at least 100%) of a target pathogen in an in vitro assay.

Bacteria compositions provided herein may stimulate human keratinocytes.Such stimulation may occur in vivo and/or in vitro. Bacteria canstimulate keratinocytes by increasing the transcription of the mRNA ofimmune mediators or molecules involved in epithelial barrier functionincluding, for example, increasing production of an mRNA-encoding IL-1β,an mRNA-encoding defensin beta 4, an mRNA-encoding Cyp27b1, anmRNA-encoding a vitamin D receptor, an mRNA-encoding occludin, anmRNA-encoding claudin 1, and/or an mRNA-encoding filaggrin. Bacterialcompositions described herein may induce cytokine expression from humancells. Exemplary impacted human cells include, without limitation, thecells of the skin, such as fibroblasts and keratinocytes. Exemplaryinduced cytokines include, without limitation, an interleukin (IL), suchas IL-6 and IL-1β.

In some embodiments, bacteria from only a single genus are included in acomposition for treatment of a skin condition associated with dysbiosis.In alternative embodiments, combinations of genera are included in acomposition for treatment of a skin condition associated with dysbiosis.In further embodiments, the composition comprises bacteria that areviable. Compositions described herein may include, for example, 1, 2, 3,4, or 5 genera of bacteria.

Bacteria described herein for treatment of a skin condition associatedwith dysbiosis may be gram-positive bacteria or gram-negative bacteria.Exemplary gram-positive bacteria include a Staphylococcus speciesincluding, without limitation, Staphylococcus epidermis, Staphylococcuscohnii, and Staphylococcus hominis. Exemplary gram-negative bacteriainclude, without limitation, Proteobacteria, Acetobacteraceae,Spirochaetaceae, Enterobacteriales, Fusobacterium polymorphum, andSelenomonadales. Exemplary genera of gram-negative bacteria additionallyinclude Pseudomonas, Pantoea, Moraxella, Roseomonas, Vitreoscilla, andMethylobacteria spp. The gram-negative bacteria may be diplococci,coccobacilli, cocci, or bacilli. Additional bacteria for treatment of askin condition associated with dysbiosis include, without limitation,Lactobacillus casei var. rhamnosus, Bifidobacterium animalis subsplactis. Bifidobacterium longum, Lactobacillus plantarum, andLactobacillus johnsonii.

In some embodiments, a composition provided herein comprises a viablespecies of Roseomonas. In some embodiments, a composition providedherein comprises a viable species of Pseudomonas. In some embodiments, acomposition provided herein comprises a viable species of Roseomonas andviable species of Pseudomonas.

Compositions described herein may include one or more of a species ofthe Roseomonas genus for treatment of a skin condition associated withdysbiosis. Exemplary species of the Roseomonas genus include, withoutlimitation, Roseomonas aerilata, Roseomonas aerophila, Roseomonasaestuarii, Roseomonas alkaliterrae, Roseomonas aquatic, Roseomonascervicalis, Roseomonas fauriae, Roseomonas frigidaquae, Roseomonasgilardii, Roseomonas lacus, Roseomonas ludipueritiae, Roseomonas mucosa,Roseomonas pecuniae, Roseomonas rhizosphaerae, Roseomonas riguiloci,Roseomonas rosea, Roseomonas soli, Roseomonas stagni, Roseomonas terrae,and Roseomonas vinacea. In some instances, the Roseomonas mucosa is, oris derived from, ATCC BAA-692 strain. The bacteria may be viable. Thebacteria may be isolated and/or purified. The bacteria may be isolatedfrom a subject not having the skin condition associated with thedysbiosis which is sought to be treated.

Compositions described herein may include one or more of a species ofthe Pseudomonas genus for treatment of a skin condition associated withdysbiosis. Exemplary species of the Pseudomonas genus include, withoutlimitation, Pseudomonas aeruginosa, Pseudomonas luteola, and Pseudomonasoryzihabitans. The bacteria may be viable. The bacteria may be isolatedand/or purified. The bacteria may be isolated from a subject not havingthe skin condition associated with dysbiosis which is sought to betreated.

Compositions described herein may include one or more of a species ofthe Pantoea genus for treatment of a skin condition associated withdysbiosis. Exemplary species of the Pantoea genus include, withoutlimitation, Pantoea septica. The bacteria may be viable. The bacteriamay be isolated and/or purified. The bacteria may be isolated from asubject not having the skin condition associated with dysbiosis which issought to be treated.

Compositions described herein may include one or more of a species ofthe Moraxella genus for treatment of a skin condition associated withdysbiosis. Exemplary species of the Moraxella genus include, withoutlimitation, Moraxella osloensis. The bacteria may be viable. Thebacteria may be isolated and/or purified. The bacteria may be isolatedfrom a subject not having the skin condition associated with dysbiosiswhich is sought to be treated.

Compositions described herein may include one or more of a species ofthe Vitreoscilla genus for treatment of a skin condition associated withdysbiosis. Exemplary species of the Vitreoscilla genus include, withoutlimitation, Vitreoscilla filiformis, Vitreoscilla beggiatoides, andVitreoscilla beggiatoides. The bacteria may be viable. The bacteria maybe isolated and/or purified. The bacteria may be isolated from a subjectnot having the skin condition associated with dysbiosis which is soughtto be treated.

Bacteria of a single species or a single strain can be included incompositions disclosed herein. Combinations of species bacteria can beincluded in compositions for use in disclosed methods. Thus, acomposition described herein can include 1, 2, 3, 4, or 5 species ofbacteria. In some embodiments, a composition provided herein includesmultiple viable Roseomonas mucosa strains from one or more subjects nothaving a skin condition associated with dysbiosis. In some embodiments,a composition provided herein includes multiple viable Pseudomonasaeruginosa strains from one or more donor subjects not having a skincondition associated with dysbiosis. In some embodiments, a compositionprovided herein includes a viable strain of Roseomonas mucosa and aviable strain of Pseudomonas aeruginosa one or more donor subjects nothaving a skin condition associated with dysbiosis. Exemplary skinconditions associated with dysbiosis include, without limitation,eczema, allergic eczema, flexural eczema, infantile eczema, nummulareczema, discoid lupus, prurigo Besnier, psoriasis, vitiligo, dermatitis,atopic dermatitis, perioral dermatitis, neurodermatitis, seborrheicdermatitis, rosacea, and acne

Compositions provided herein for treatment of a condition associatedwith skin dysbiosis may include one or more types of bacteria. Acomposition provided herein may comprise 1 to 15, 2 to 12, 2 to 10, or 2to 5 different species of bacteria. A composition provided herein maycomprise 1 to 15, 2 to 12, 2 to 10, or 2 to 5 different strains ofbacteria. A composition provided herein may comprise 1 to 15, 2 to 12, 2to 10, or 2 to 5 different strains of the same species of bacteria. Thecomposition provided herein may comprise 1, 2, 3, 4 or 5 differentstrains of the same species of bacteria. The composition provided hereinmay comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more different species ofbacteria. In some instances, a composition provided herein can compriseat least 2, at least 3, at least 4, at least 5, at least 6, at least 7,at least 8, at least 9, at least 10, at least 11, at least 12, at least13, at least 14, at least 15, at least 16, at least 17, at least 18, atleast 19, at least 20, at least 30, at least 40, at least 50, or greaterthan 50 types of bacteria, as defined by genus, species, or operationaltaxonomic unit (OTU). Strains described herein may be gram negative orgram positive. Such strains may be derived from a donor that does nothave a certain dysbiosis of the skin for which the strain is to be usedto treat.

Bacteria described herein may be transformed with a heterologous nucleicacid, such as in the form of a plasmid. For example, the plasmid maycomprise an expression vector encoding for protein of interest. Such amechanism provides a means for introduction of exogenous DNA can beintroduced bacterial cells with standard techniques, such aselectroporation or calcium phosphate-mediated transfection.

In some embodiments, the heterologous nucleic acid is included in aplasmid. A plasmid generally contains multiple genetic elementspositionally and sequentially oriented with other necessary geneticelements, such that the nucleic acid in a nucleic acid cassette can betranscribed and when necessary translated in the transfected cells.Plasmids can include nucleic acids that are derived from DNA via aplasmid vector, cosmids, or phagemids, where one or more heterologousnucleic acid can be inserted. The heterologous nucleic acid can encode aprotein of interest, which can be operably-linked to a promoter forexpression of the bacteria.

Plasmids generally contain one or more unique restriction sites. Inaddition, a plasmid can confer well-defined phenotypes on the hostorganism, which can be selectable or readily-detected, for example, drugresistance. Thus, the plasmid can include an expression cassette, wherea polypeptide is encoded. Expression can include the efficienttranscription of an inserted gene, nucleic acid sequence, or nucleicacid cassette with the plasmid.

In some embodiments, when a circular plasmid is transferred into abacterial cell, the plasmid can be an autonomously replicating,extra-chromosomal DNA molecule, distinct from the normal bacterialgenome and non-essential for bacterial cell survival under non-selectiveconditions. Persistent expression can refer to introduction of genesinto the cell together with genetic elements which enable episomal(extra-chromosomal) replication and/or maintenance of the geneticmaterial in the cell. Persistent expression can lead to apparentlystable transformation of the cell without the integration of the novelgenetic material into the chromosome of the host cell. A plasmid canalso introduce genetic material into chromosomes of the targeted cell.Gene expression after stable introduction can permanently alter thecharacteristics of the cell and cell progeny by replication leading tostable transformation.

Heterologous nucleic acids described herein may provide for increasedproduction of a metabolite that is increased in production from bacteriaof skin from a healthy donor subject in comparison to a similar strainof the bacteria from a subject having a skin condition associated withdysbiosis. Heterologous nucleic acids described herein may provide fordecreased production of a metabolite that is decreased in productionfrom bacteria of skin from a healthy donor subject in comparison to asimilar strain of the bacteria from a subject having a skin conditionassociated with dysbiosis. Mechanisms for decreasing production mayinclude, without limitation, gene silencing or knockdown, e.g., siRNA,shRNA, RNAi, or CRISPR/Cas mechanisms.

Methods for producing bacterial strains for incorporation in acomposition described herein optionally include processing steps oforganism banking, organism production, and preservation. For organismbanking, strains of bacteria can be isolated directly from a specimen,for example, from human skin or a banked stock. Bacteria can be culturedon a nutrient agar or broth that supports growth to generate viablebiomass. The cultured biomass can be preserved in multiple aliquots forlong-term storage. Bacteria may be isolated directly from the skin of ahuman donor subject. Generally, the human donor subject does not have askin condition associated with dysbiosis, e.g., atopic dermatitis, orany other skin condition. Bacteria can also be isolated from othersources including, for example, commercial sources or environmentalsamples.

Microbial Metabolites

Certain strains or species of bacteria have been reported to have atherapeutic effect on skin conditions associated with dysbiosis. Thetherapeutic effect of such bacteria may be attributed to the metabolicprofile of the bacteria, i.e. metabolite produced by the bacteria. Insome instances, bacteria can produce lipids that have a beneficialeffect on restoring barrier function and regulating immune response.

Provided herein are compositions and methods for therapy for treatmentof a skin condition associated with dysbiosis by administration of oneor more metabolites which alleviates the condition. The one or moremetabolites which alleviate the skin condition associated with dysbiosismay be those which are increased in production from a species ofbacteria present on the skin of an individual without the skin conditionas compared to the species of bacteria from an individual having theskin condition. The one or more metabolites may be part of a combinationtherapy also including a species of bacteria obtained or derived from adonor subject that does not have the skin condition associated withdysbiosis. For example, the metabolite can be obtained from a species ofbacteria obtained or derived from donor subject that does not have theskin condition associated with dysbiosis. Metabolites described hereinfor treatment of a skin disease associated with dysbiosis for use in acomposition described herein include, without limitation, those listedin Table 1. Provided herein are methods for treatment of a skincondition associated with dysbiosis comprising administering to asubject in need thereof a composition comprising metabolites listed inTable 1, optionally in addition to administration of one or more speciesof bacteria described herein for treatment of the skin condition. Whenmetabolite administration is part of a co-therapy, the metabolite canenhance the therapeutic effect of the one or more bacteria administered.Exemplary skin conditions associated with dysbiosis include, withoutlimitation, eczema, allergic eczema, flexural eczema, infantile eczema,nummular eczema, discoid lupus, prurigo Besnier, psoriasis, vitiligo,dermatitis, atopic dermatitis, perioral dermatitis, neurodermatitis,seborrheic dermatitis, rosacea, and acne.

TABLE 1 Metabolites Category Metabolite Lipids PhosphatidylethanolaminePhosphatidylethanolamine 36:2 Phosphatidylethanolamine 14:0/20:1Phosphatidylethanolamine 22:1/14:1 Phosphatidylethanolamine 36:2Phosphatidylcholine Phosphatidylcholine 37:0 Phosphatidylcholine 37:2Phosphatidylcholine 38:2 Phosphatidylcholine(18:2(9Z,12Z)/18:0)Lysophosphatidylcholine 8-keto palmitic acid Peptide Tyr-Leu-Arg Sugarmaltopentaose Nucleic acid, nucleoside, 2′-deoxyguanosine5′-monophosphate or nucleotide Additional metabolitesN4-acetylaminobutanal 5-ethylpentadecane-2,4-dione Ricinoleic acidmethyl ester Trenbolone acetateN-(2-hydroxyethyl)-11(12)-epoxy-5Z,8Z,14Z- eicosatrienamide

Combination Therapies

Provided herein are combination therapies for treatment of a skincondition associated with dysbiosis. In a first design, the combinationtherapy includes administration of a first therapeutic agent, whereinthe first therapeutic agent comprises one or more metabolites, and asecond therapeutic agent for treatment of the skin condition, whereinthe combination of administering the therapeutic agents provides for anenhanced therapeutic effect than administration of either agent alone.In further instances, the first therapeutic agent is present in anamount to increase the therapeutic effect of the second therapeuticagent. In some instances, one or more metabolites enhance thetherapeutic effect of a second therapeutic agent. Exemplary metabolitesare described herein, including those listed in Table 1. The combinationtherapy may further include administration of a third therapeutic agentfor treatment of the skin condition. Exemplary therapeutic agents forinclusion are listed in Table 2. In a second design, the combinationtherapy includes administration of a first therapeutic agent, whereinthe first therapeutic agent comprises a species or strain of bacteriadescribed herein for treatment of a skin condition associated withdysbiosis, and a second therapeutic agent for treatment of the skincondition, where the second therapeutic agent is listed in Table 2, andwherein the combination of therapeutic agents provides for an enhancedtherapeutic effect than administration of either agent alone. In furtherinstances, the first therapeutic agent is present in an amount toincrease the therapeutic effect of the second therapeutic agent, or viceversa. In some embodiments, the combination therapy further includes amixture of live bacteria, wherein the mixture comprises: at least onestrain of gram negative bacteria derived from a donor that does not haveskin dysbiosis; and at least one strain of gram positive bacteriaderived from a second donor that does not have skin dysbiosis, whereinthe at least one strain of gram negative bacteria and the at least onestrain of gram positive bacteria are present in an amount sufficient fortreatment of skin dysbiosis in a subject in need thereof.

Provided herein are compositions for treatment of a skin conditionassociated with dysbiosis, comprising a metabolite, wherein themetabolite is present in an amount sufficient to reduce atopicdermatitis in a subject in need thereof, and wherein the metabolite isproduced from a species of gram-negative bacteria that is more highlyabundant in skin from a subject that does not have atopic dermatitis ascompared to abundance of the species in skin from a subject havingatopic dermatitis; a first agent that is a gram positive bacterialstrain; and a second agent that is a gram negative bacterial strain.

Combination therapies described herein may include donor derivedbacterial strains, where the donor does not show signs of a skincondition associated with dysbiosis. In some instances, compositions forcombination therapy described herein comprise a plurality of strains foreach species included in the composition. In some instances, thecombination of therapeutic agents provides for a therapeutic effect thatis enhanced compared to administration of any one agent in the mixturealone. In some instances, a strain of gram positive bacteria is selectedbased on an increase relative abundance compared the same species ofbacteria in a subject suffering from a skin condition associated withdysbiosis. Exemplary gram positive bacterial species for inclusion are,without limitation, one or more species in the genus of Staphylococci,Streptococci, Enterococci, Corynebacteriae, or Propionibacterii.Exemplary Staphylococci species for combination with a gram negativespecies described herein include, without limitation, Staphylococcusaureus, Staphylococcus hemolyticus, Staphylococcus auricularis,Staphylococcus warneri, Staphylococcus hominis, Staphylococcusepidermidis, Staphylococcus simulans, Staphylococcus sciuri,Staphylococcus capitis, Staphylococcus saprophyticus, Staphylococcusxylosis, Staphylococcus cohnii, and Staphylococcus lentus. ExemplaryStreptococci species for combination with a gram negative speciesdescribed herein include, without limitation, Streptococcus bovis,Streptococcus agalactae, Streptococcus viridian, Streptococcuspneumonia, Streptococcus salivarius, and Streptococcus acidominimus.Exemplary Enterococci species combination with a gram negative speciesdescribed herein include, without limitation, Enterococcus faecalis,Enterococcus Faecium, and Enterococcus gallinarium. ExemplaryCorynebacteriae species for combination with a gram negative speciesdescribed herein include, without limitation, Corynebacterium xerosisand Corynebacterium minutissimum. Exemplary Propionibacterium speciesfor combination with a gram negative species described herein include,without limitation, Propionibacterium acnes. Exemplary gram positivebacteria for combination with a gram negative species described hereininclude, without limitation, Staphylococcus epidermidis, Staphylococcushominis, Staphylococcus cohnii, or Propionibacterium acnes. In someinstances, the Staphylococcus epidermidis is, or is derived from, ATCC12228 strain. In some instances, the Propionibacterium acnes is, or isderived from, ATCC 6919 strain. Exemplary genera of gram-negativebacteria additionally include Pseudomonas, Pantoea, Moraxella,Roseomonas, Vitreoscilla, and Methylobacteria spp. Exemplary species ofthe Roseomonas genus include, without limitation, Roseomonas aerilata,Roseomonas aerophila, Roseomonas aestuarii, Roseomonas alkaliterrae,Roseomonas aquatic, Roseomonas cervicalis, Roseomonas fauriae,Roseomonas frigidaquae, Roseomonas gilardii, Roseomonas lacus,Roseomonas ludipueritiae, Roseomonas mucosa, Roseomonas pecuniae,Roseomonas rhizosphaerae, Roseomonas riguiloci, Roseomonas rosea,Roseomonas soli, Roseomonas stagni, Roseomonas terrae, and Roseomonasvinacea. Exemplary species of the Pseudomonas genus include, withoutlimitation, Pseudomonas aeruginosa, Pseudomonas luteola, and Pseudomonasoryzihabitans. Exemplary species of the Pantoea genus include, withoutlimitation, Pantoea septica. Exemplary species of the Moraxella genusinclude, without limitation, Moraxella osloensis. Exemplary species ofthe Vitreoscilla genus include, without limitation, Vitreoscillafiliformis, Vitreoscilla beggiatoides, and Vitreoscilla beggiatoides.

Therapeutic agents may be, without limitation, a microorganism, smallmolecule, antibody, calcineurin inhibitor, immune modulator, or steroid.Examples of such agents are provided, without limitation, in Table 2.Each of the first, second, or third therapeutic agents may beadministered simultaneously or sequentially. Each of the first, second,or third therapeutic agents may be administered in similar or differentdosage forms (oral, rectal, or topical). Exemplary skin conditionsassociated with dysbiosis include, without limitation, eczema, allergiceczema, flexural eczema, infantile eczema, nummular eczema, discoidlupus, prurigo Besnier, psoriasis, vitiligo, dermatitis, atopicdermatitis, perioral dermatitis, neurodermatitis, seborrheic dermatitis,rosacea, and acne.

TABLE 2 Therapeutic agents. Type Description Microorganism Roseomonasmucosa (optionally obtained Pseudomonas aeruginosa from or derived froma Pantoea septica donor subject not having Vitreoscilla filiformis askin condition Vitreoscilla beggiatoides associated with dysbiosis)Vitreoscilla beggiatoides Moraxella osloensis Lactobacillus casei var.rhamnosus Bifidobacterium animalis subsp lactis. Bifidobacterium longumLactobacillus plantarum Lactobacillus johnsonii Staphylococcus epidermisStaphylococcus cohnii Staphylococcus hominis Propionibacterium acnesCalcineurin inhibitors Cyclosporine Pimecrolimus Tacrolimus VoclosporinAntibody Omalizumab Ligelizumab Ustekinumab Lebrikizumab TralokinumabSecukinumab Nemolizumab Dupilumab Mepolizumab Fezakinumab GBR 830Tezepelumab Immune modulators Cyclosporine Methotrexate AzathioprineMycophenolic acid Mycophenolate mofetil Thymic stromal lymphopoietin(TSLP) antagonists OX40 antagonists Small Molecules FevipiprantTimapiprant Baricitinib AQX-1125 Aprimelast Serlopitant TradipitantAsimadoline Tofacitinib Upadacitinib PF-04965842 Steroid CorticosteroidsBetamethasone dipropionate Betamethasone valerate DesonideDesoximetasone Diflorasone diacetate Fluocinonide FlurandrenolideFlurandrenolide Fluticasone propionate Fluocinolone acetonideHydrocortisone Amcinonide Halcinonide Triamcinolone TriamcinoloneAcetonide Mometasone AlclometasoneTherapeutic Applications: Skin Conditions Associated with Dysbiosis

Provided herein are methods and compositions for the treatment of skinconditions associated with dysbiosis. Such conditions are oftenassociated with a disruption in the skin barrier and inflammation inregions of the skin. Affected subjects may have a rash, itchiness,redness, swelling, vesicle formation (minute blisters), cracking,weeping, crusting, and scaling of the skin. Compositions and methodsdescribed herein for treatment of the skin condition associated withdysbiosis may experience a lessening of the rash, itchiness, redness,swelling, vesicle formation (minute blisters), cracking, weeping,crusting, or scaling of the skin associated with the skin condition.Exemplary skin conditions associated with dysbiosis include, withoutlimitation, eczema, allergic eczema, flexural eczema, infantile eczema,nummular eczema, discoid lupus, prurigo Besnier, psoriasis, vitiligo,dermatitis, atopic dermatitis, perioral dermatitis, neurodermatitis,seborrheic dermatitis, rosacea, and acne. Treatments described hereinmay also provide for treatment of secondary disease conditionsassociated with the primary disease being treated. For example, in thecase of treating atopic dermatitis, a composition described herein alsoprovides for treatment or prevention of asthma, allergies, and allergicrhinitis (hay fever).

Dosage Forms

Compositions and pharmaceutical compositions provided herein may beformulated for topical, oral, or rectal administration. FIG. 1A depictsa route of topical administration for bacteria 101 and metabolites 102,or a route of oral administration for bacteria 103, and FIG. 1B depictsa route of rectal administration for bacteria 104. Exemplary oral dosageforms include, without limitation, a tablet, lozenge, pastille capsule,tab, granules, powder, liquid, emulsion, suspension and syrup. Exemplaryrectal dosage forms include, without limitation, a suppository, andenema solution, rectal foam, or rectal gel. Exemplary topical dosageforms include, without limitation, creams, ointments, lotions, andsterile aqueous solutions or suspensions. Compositions can include anaqueous carrier, and be applied as a spray to the skin.

Creams are viscous liquids or semisolid emulsions, either oil-in-wateror water-in-oil. Cream bases are water-washable, and contain an oilphase, an emulsifier, and an aqueous phase.

The oil or “internal” phase generally contains of petrolatum and a fattyalcohol, such as acetyl or stearyl alcohol. The aqueous phase can exceedthe oil phase in volume, and can contain a humectant. The emulsifier ina cream formulation can be a nonionic, anionic, cationic, or amphotericsurfactant.

Lotions can include preparations to be applied to the skin surfacewithout friction. Lotions are typically liquid or semiliquidpreparations in which particles are present in a water or alcohol base.Lotions can be suspensions of solids or a liquid oily emulsion of theoil-in-water type. Lotions can be used for treating large body areas,because of the ease of applying a more fluid composition. It isgenerally necessary that the insoluble matter in a lotion be finelydivided. Lotions typically contain suspending agents to produce betterdispersions as well as compounds useful for localizing and holding theactive agent in contact with the skin, e.g., methylcellulose, sodiumcarboxymethyl-cellulose, or the like.

Solutions are homogeneous mixtures prepared by dissolving one or morechemical substances (solutes) in a liquid such that the molecules of thedissolved substance are dispersed among those of the solvent. Thesolution can contain other pharmaceutically or cosmetically acceptablechemicals to buffer, stabilize, or preserve the solute. Common examplesof solvents used in preparing topical solutions are ethanol, water,propylene glycol or any other-acceptable vehicles. These can be appliedin any manner, such as spraying them on the skin, painting them on theskin, or wetting a bandage with the solution.

Gels are semisolid, suspension-type systems. Single-phase gels containorganic macromolecules distributed substantially uniformly throughoutthe carrier liquid, which can be aqueous, contain an alcohol, orhydrophobic. Organic macromolecules, including gelling agents, can becrosslinked acrylic acid polymers, e.g., carboxypolyalkylenes(CARBOPOL®). Non-limiting examples of gels include hydrophilic polymers,such as polyethylene oxides, polyoxyethylene-polyoxypropylenecopolymers, and polyvinylalcohol; cellulosic polymers, such ashydroxypropyl cellulose, hydroxyethyl cellulose, hydroxypropylmethylcellulose, hydroxypropyl methylcellulose phthalate, and methylcellulose; gums, such as tragacanth and xanthan gum; sodium alginate;and gelatin. To prepare a uniform gel, dispersing agents, such asalcohol or glycerin can be added, or the gelling agent can be dispersedby trituration, mechanical mixing or stirring, or combinations thereof.

Ointments can also be used in the disclosed methods. Ointments aresemisolid preparations that are typically based on petrolatum or otherpetroleum derivatives. The specific ointment base to be used, as will beappreciated by those skilled in the art, is one that will provide for anumber of desirable characteristics, e.g., emolliency or the like. Anointment base is generally inert, stable, non-irritating, andnon-sensitizing. Ointment bases may be oleaginous bases, emulsifiablebases, emulsion bases, or water-soluble bases.

Oleaginous ointment bases include, for example, vegetable oils, fatsobtained from animals, and semisolid hydrocarbons obtained frompetroleum. Emulsifiable ointment bases, also known as absorbent ointmentbases, contain little or no water and include, for example,hydroxystearin sulfate, anhydrous lanolin, and hydrophilic petrolatum.Emulsion ointment bases are either water-in-oil (W/O) emulsions oroil-in-water (O/W) emulsions, and include, for example, acetyl alcohol,glyceryl monostearate, lanolin, and stearic acid. Water-soluble ointmentbases are prepared from polyethylene glycols of varying molecularweight.

Pastes are semisolid dosage forms in which the active agent is suspendedin a suitable base, and are also of use. Depending on the nature of thebase, pastes are divided between fatty pastes or those made fromsingle-phase aqueous gels. The base in a fatty paste can be petrolatumor hydrophilic petrolatum or the like. The pastes made from single-phaseaqueous gels can incorporate carboxymethylcellulose or the like as abase.

A topical composition can be any form suitable for application to thebody surface including, for example, as a cream, lotion, spray,solution, gel, foam, ointment, paste, plaster, paint, bioadhesive,bandage, spray, suspension, and containing liposomes, micelles, and/ormicrospheres. A topical composition can be used in combination with anocclusive overlayer so that moisture evaporating from the body surfacecan be maintained within the formulation upon application to the bodysurface and thereafter. A cream, lotion, gel, ointment, paste, or thelike can be spread on the affected surface.

A solution can be applied in the same way, but more typically will beapplied with a dropper, swab, sprayer or the like, and carefully appliedto the affected areas. Compositions can be applied directly to thetarget location, for example in a topical preparation, such as anointment, or as a part of a dressing or a bandage. Compositions can beformulated as a unit dosage, for administration by any device foradministration to the skin. The unit dosage can be a reservoir of theactive agent in a carrier, for example an adhesive carrier capable ofadhering to the skin for a desired period of time, such as at least aday or more.

Pharmaceutical compositions provided herein may include apharmaceutically-acceptable carrier, and can include additionalcompounds. In some embodiments, pharmaceutical compositions includeadditional active and/or inactive materials, which can be in prepared assingle dosage unit or in a multi-dose format.

Pharmaceutical compositions described herein may include a carrier thatcomprises one or more of a buffering agent, a preservative, astabilizer, a binder, a compaction agent, a lubricant, a dispersionenhancer and/or a coloring agent. Non-limiting examples of suitablebuffering agents include sodium citrate, magnesium carbonate, magnesiumbicarbonate, calcium carbonate, and calcium bicarbonate. Non-limitingexamples of suitable preservatives include antioxidants, such as alphatocopherol and ascorbate, parabens, chlorobutanol, and phenol.Non-limiting examples of suitable binders include sucrose, starches,pregelatinized starches, gelatin, polyvinylpyrrolidone, cellulose,methylcellulose, sodium carboxymethylcellulose, ethylcellulose,polyacrylamides, polyvinyloxoazolidone, polyvinylalcohols, C12-C18 fattyacid alcohol, polyethylene glycol, polyols, saccharides,oligosaccharides, and combinations thereof. Non-limiting examples ofsuitable lubricants include magnesium stearate, calcium stearate, zincstearate, hydrogenated vegetable oils, sterotex, polyoxyethylenemonostearate, talc, polyethyleneglycol, sodium benzoate, sodium laurylsulfate, magnesium lauryl sulfate, and light mineral oil. A pH bufferingagent(s) can, if employed and when dissolved in an aqueous component ofthe composition, provide a pH in the range of 5 to 7 (5 e.g. about pH5.5).

Pharmaceutical compositions described herein may include a carrier thatcomprises other ingredients including, for example, ingredients thatsustain growth of the bacteria. In some embodiments, pharmaceuticalcompositions can include a nutrient. In some embodiments, compositionsinclude at least one carbohydrate or saccharide. A carbohydrate can be amonosaccharide, a disaccharide, trisaccharide, oligosaccharide, orpolysaccharide. Non-limiting examples of carbohydrates include glucose,sucrose, galactose, mannose, ribose, arabinose, xylose, fructose,maltose, cellobiose, lactose, raffinose, stachyose, starch, glycogen,and cellulose. Carbohydrates can contain modified saccharide unit,including, for example, 2′-deoxyribose in which a hydroxyl group isremoved, 2′-fluororibose in which a hydroxyl group is replaced with afluorine, and or N-acetylglucosamine, a nitrogen-containing form ofglucose (e.g., 2′-fluororibose, deoxyribose, and hexose). Carbohydratescan exist in many different forms, for example, conformers, cyclicforms, acyclic forms, stereoisomers, tautomers, anomers, and isomers.

Pharmaceutical compositions described herein may include a carrier thatcomprises one or more lipids. A lipid can include fats, oils,triglycerides, cholesterol, phospholipids, and fatty acids. Fats, oils,and fatty acids can be saturated, unsaturated (cis or trans), orpartially unsaturated (cis or trans). Non-limiting examples of fattyacids include lauric acid (12:0), myristic acid (14:0), palmitic acid(16:0), palmitoleic acid (16:1), margaric acid (17:0), heptadecenoicacid (17:1), stearic acid (18:0), oleic acid (18:1), linoleic acid(18:2), linolenic acid, α-linolenic acid, and γ-linolenic acid.

Pharmaceutical compositions described herein may include a carrier thatcomprises at least one supplemental mineral or mineral source.Non-limiting examples of minerals include chloride, sodium, calcium,iron, chromium, copper, iodine, zinc, magnesium, manganese, molybdenum,phosphorus, potassium, and selenium. Suitable forms of any of theforegoing minerals include soluble mineral salts, slightly solublemineral salts, insoluble mineral salts, chelated minerals, mineralcomplexes, non-reactive minerals, such as carbonyl minerals, and reducedminerals, and combinations thereof. In some embodiments, compositionsinclude at least one supplemental vitamin. Supplemental vitamins can befat-soluble or water-soluble. Non-limiting examples of vitamins includevitamin C, vitamin A, vitamin E, vitamin B12, vitamin K, riboflavin,niacin, vitamin D, vitamin B6, folic acid, pyridoxine, thiamine,pantothenic acid, and biotin. Suitable forms of any of the foregoing aresalts of the vitamin, derivatives of the vitamin, compounds having thesame or similar activity of the vitamin, and metabolites of the vitamin.

Various other additives can be included in the compositions.Non-limiting examples of additives include antioxidants, astringents,perfumes, preservatives, emollients, pigments, dyes, humectants,propellants, and sunscreen agents, as well as other classes of materialswhose presence can be pharmaceutically or otherwise desirable.Non-limiting examples of optional additives include preservatives, suchas sorbate; solvents, such as isopropanol and propylene glycol;astringents, such as menthol and ethanol; emollients, such aspolyalkylene methyl glucosides; humectants, such as glycerin;emulsifiers, such as glycerol stearate, PEG-100 stearate, polyglyceryl-3hydroxylauryl ether, and polysorbate 60; sorbitol and otherpolyhydroxyalcohols, such as polyethylene glycol; sunscreen agents, suchas octyl methoxyl cinnamate (Parsol MCX) and butyl methoxybenzoylmethane (Parsol 1789); antioxidants, such as ascorbic acid(vitamin C), α-tocopherol (Vitamin E), β-tocopherol, γ-tocopherol,δ-tocopherol, ε-tocopherol, ζ₁-tocopherol, ζ₂-tocopherol, η-tocopherol,and retinol (vitamin A); essential oils, ceramides, essential fattyacids, mineral oils, vegetable oils (e.g., soya bean oil, palm oil,liquid fraction of shea butter, sunflower oil), animal oils (e.g.,perhydrosqualene), synthetic oils, silicone oils or waxes (e.g.,cyclomethicone and dimethicone), fluorinated oils (generallyperfluoropolyethers), fatty alcohols (e.g., cetyl alcohol), and waxes(e.g., beeswax, carnauba wax, and paraffin wax); skin-feel modifiers;and thickeners and structurants, such as swelling clays and cross-linkedcarboxypolyalkylenes.

Other additives include materials that condition the skin. Suchmaterials can soften the skin by retarding the decrease of water contentof the skin and/or protect the skin. Conditioners and moisturizingagents include, for example, pyrrolidine carboxylic acid and aminoacids; organic antimicrobial agents, such as triclosan and benzoic acid.Further additives include anti-inflammatory agents, such asacetylsalicylic acid and glycyrrhetinic acid; anti-seborrhoeic agents,such as retinoic acid; vasodilators, such as nicotinic acid; inhibitorsof melanogenesis, such as kojic acid; and mixtures thereof.

In some embodiments, compositions described herein include alphahydroxyacids, alpha ketoacids, polymeric hydroxyacids, moisturizers,collagen, marine extract, and antioxidants, such as ascorbic acid(vitamin C) and α-tocopherol (Vitamin E). Sunscreens can also beincluded. Additional, components, such as enzymes, herbs, plantextracts, and glandular or animal extracts can be added to thecomposition. The amounts of these various additives are thoseconventionally used in the cosmetics field, and range, for example, fromabout 0.01% to about 20% of the total weight of the topical formulation.

Compositions described herein can also include antimicrobial agents, toprevent spoilage upon storage, for example, to inhibit growth ofmicrobes, such as yeasts and molds. Suitable antimicrobial agents aretypically selected from the group consisting of the methyl and propylesters of p-hydroxybenzoic acid (i.e., methyl and propyl paraben),sodium benzoate, sorbic acid, imidurea, and combinations thereof.

Compositions described herein can also contain irritation-mitigatingadditives to reduce or eliminate the possibility of skin irritation orskin damage resulting from the chemical entity to be administered, orother components of the composition. Suitable irritation-mitigatingadditives include, for example, a-tocopherol; monoamine oxidaseinhibitors, particularly phenyl alcohols, such as 2-phenyl-1-ethanol;glycerin; salicylates; ascorbates; ionophores, such as monensin;amphiphilic amines; ammonium chloride; N-acetylcysteine; capsaicin; andchloroquine. The irritation-mitigating additive, if present, can beincorporated into the compositions at a concentration effective tomitigate irritation or skin damage, typically representing not more thanabout 20 wt %, more typically not more than about 5 wt %, of theformulation. Non-limiting examples of suitable pharmacologically-activeagents that can be incorporated into the present formulations caninclude the following: agents that improve or eradicate pigmented ornon-pigmented age spots, keratoses, and wrinkles; local anesthetics andanalgesics; corticosteroids; retinoids; and hormones. Some examples oftopical pharmacologically-active agents include acyclovir,amphotericins, chlorhexidine, clotrimazole, ketoconazole, econazole,miconazole, metronidazole, minocycline, phenytoin, para-amino benzoicacid esters, octyl methoxycinnamate, octyl salicylate, oxybenzone,dioxybenzone, tocopherol, tocopheryl acetate, zinc pyrithione,diphenhydramine, pramoxine, lidocaine, procaine, crotamiton,hydroquinone and its monomethyl and benzyl ethers, naproxen, ibuprofen,cromolyn, retinol, retinyl palmitate, retinyl acetate, coal tar,griseofulvin, estradiol, hydrocortisone, hydrocortisone 21-acetate,hydrocortisone 17-valerate, hydrocortisone 17-butyrate, progesterone,betamethasone valerate, betamethasone dipropionate, triamcinoloneacetonide, fluocinonide, clobetasol propionate, minoxidil, dipyridamole,diphenylhydantoin, benzoyl peroxide, 5-fluorouracil, tacrolimus, andtopical steroids, such as alclometasone, amcinonide, betamethasone,clobetasol, desonide, dexoximetasone, diflorasone, flucinonide,flurandrenolide, halobetasol, halcinonide, hydrocortisone, and/ortriamcinolone.

Although topical formulations, such as creams and salves, are formulatedfor dermal delivery, the delivery systems can include time-release,delayed release, or sustained release delivery systems. Such systems canavoid repeated administrations of the compositions, increasingconvenience to the subject and the physician. Non-limiting examples ofrelease delivery systems include (a) erosional systems and (b)diffusional systems in which an active component permeates at acontrolled rate from a polymer. The delivery system can includecollagen, fibrin, or a membrane extract, such as a basal membraneextract, for example, in which compositions are formulated foradministration to the skin. Suitable basement membrane extracts includea biologically active polymerizable extract containing in parts byweight about 60-85% laminin, 5-30% collagen IV, 1-10% nidogen, 1-10%heparan sulfate proteoglycan, and 1-5% entactin. BME can support normalgrowth and differentiation of various cell types including epithelialcells when cultured. Basal membrane extracts are well known in the artand are commercially available.

Compositions described herein may comprise a single (unit) dose ofbacteria. Compositions described herein may comprise 10³ to 10¹² colonyforming units (cfu) of bacteria or a bacterial strain described herein.Compositions described herein may comprise about 10³ to 10¹¹ cfu, 10³ to10¹⁰ cfu, 10³ to 10⁹ cfu, 10³ to 10⁸ cfu, 10³ to 10⁷ cfu, 10³ to 10⁶cfu, 10³ to about 10⁵ cfu, 10³ to 10⁴ cfu, 10⁴ to 10¹² cfu, 10⁴ to 10¹¹cfu, 10⁴ to 10¹⁰ cfu, 10⁴ to 10⁹ cfu, 10⁴ to 10⁸ cfu, 10⁴ to 10⁷ cfu,10⁴ to 10⁶ cfu, 10⁵ to 10¹² cfu, 10⁵ to 10¹¹ cfu, about 10⁵ to about10¹⁰ cfu, 10⁶ to 10¹² cfu, 10⁷ to 10¹² cfu, 10⁸ to 10¹² cfu, 10⁹ to 10¹²cfu, 10¹⁰ to 10¹² cfu, 10¹¹ to 10¹² cfu, or 10⁶ to 10¹⁰ cfu of bacteriaor a bacterial strain described herein. In some embodiments,compositions comprise about 10³ cfu, about 10⁴ cfu, about 10⁵ cfu, about10⁶ cfu, about 10⁷ cfu, about 10⁸ cfu, about 10⁹ cfu, about 10¹⁰ cfu,about 10¹¹ cfu, or about 10¹² cfu of bacteria or a bacterial straindescribed herein.

In other embodiments, a composition described herein comprises at leastabout 0.01% by weight, at least about 0.05% by weight, at least about0.1% by weight, at least about 0.2% by weight, at least about 0.3% byweight, at least about 0.4% by weight, at least about 0.5% by weight, atleast about 0.6% by weight, at least about 0.7% by weight, at leastabout 0.8% by weight, at least about 0.9% by weight, at least about 1.0%by weight, at least about 1.5% by weight, at least about 2.0% by weight,at least about 3.0% by weight, at least about 4.0% by weight, at leastabout 5.0% by weight, at least about 6.0% by weight, at least about 7.0%by weight, at least about 8.0% by weight, at least about 9.0% by weight,at least about 10.0% by weight, at least about 11.0% by weight, at leastabout 12.0% by weight, at least about 13.0% by weight, at least about14.0% by weight, at least about 15.0% by weight, at least about 16.0% byweight, at least about 17.0% by weight, at least about 18.0% by weight,at least about 19.0% by weight, at least about 20.0% by weight, at leastabout 25.0% by weight, at least about 30.0% by weight, at least about35.0% by weight, at least about 40.0% by weight, at least about 45.0% byweight, or at least about 50.0% by weight of bacteria or bacterialstrain described herein. In some embodiments, compositions can includefrom 0.01% to 30% by weight, from about 0.01% to 20% by weight, from0.01% to 5% by weight, from 0.1% to 30% by weight, from 0.1% to 20% byweight, from 0.1% to about 15% by weight, from 0.1% to 10% by weight,from 0.1% to 5% by weight, from 0.2% to 5% by weight, from 0.3% to 5% byweight, from 0.4% to 5% by weight, from 0.5% to 5% by weight, or from 1%to 5% by weight of bacteria or bacterial strain described herein.

Administration

Subjects having a skin condition associated with dysbiosis may betreated using compositions described herein. The subject can be a human.In some embodiments, the subject is a child. The subject can be 12, 11,10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 year(s) of age. In some embodiments,the subject is an adolescent. The subject can be 12, 13, 14, 15, 16, 17,or 18 years of age. The subject is an infant or less than 1 year of age.In other embodiments, the subject is an adult. The subject can be about20 years of age, about 25 years of age, about 30 years of age, about 35years of age, about 40 years of age, about 45 years of age, about 50years of age, about 55 years of age, about 60 years of age, about 65years of age, about 70 years of age, about 75 years of age, about 80years of age, or more than 80 years of age. The subject can beimmunocompromised or can have an intact immune system (immunocompetent).

Compositions can be applied to the skin, such as at lesion areas andround lesion area, or at areas of intact skin (non-lesion areas) toprevent lesions for forming. Compositions can be used to reduce lesionsize. Compositions can be applied at one time (daily) or at multipletimes throughout the day. In some embodiments, compositions can beapplied 2 times, 3 times, 4 times, or 5 times per day. In someembodiments, compositions can be applied every other day, daily over aweek, every other day over a week, every week, 2 times per week, 3 timesper week, 4 times per week, 5 times per week, 6 times per week, or 7times per week. Compositions can be formulated as a unit dose foradministration.

For treatment of the skin, a therapeutically-effective amount of acomposition can be locally administered to the affected area. Affectedareas can include, for example, the antecubital fossa, neck, andforearm. Pharmacological compositions disclosed herein facilitate theuse of at least one species of bacteria for the treatment of atopicdermatitis. Such compositions can be suitable for delivery of the activeingredient to any suitable subject, such as, but not limited to, a humansubject, and can be manufactured in a manner that is itself known, e.g.,by means of conventional mixing, dissolving, granulating, emulsifying,encapsulating, entrapping or lyophilizing processes. Pharmacologicalcompositions can be formulated in a conventional manner using one ormore pharmacologically (physiologically or pharmaceutically) acceptablecarriers, as well as optional auxiliaries that facilitate processing ofthe active compounds into preparations which can be usedpharmaceutically, as discussed above.

Compositions and methods described herein may be used for the treatmentof a skin condition associated with dysbiosis. Treatment of the skincondition associated with dysbiosis may result in reduced lesion size,reduced number of lesions, and/or a reduction in related symptoms. Inaddition, treatment of the skin condition associated with dysbiosis witha composition or method described herein may reduce S. aureus in theskin of a subject in need thereof. Compositions and methods describedherein may provide for enhanced barrier function of the skin as measuredby trans-epidermal water loss. Administrations described herein, e.g.,topical, oral, or rectal, may reduce reoccurrences, so that additionalincidents of the skin condition associated with dysbiosis are reduced innumber, intensity, or frequency. The administration may increase thetime of remission, such as the length of time between incidents. In someembodiments, an additional incident of skin condition associated withdysbiosis does not occur for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12weeks following application. In some embodiments, an additional incidentskin condition associated with dysbiosis does not occur for 1, 2, 3, 4,5, 6, 7, 8, 9, 10, 11, or 12 months following the topical application.Exemplary skin conditions associated with dysbiosis include, withoutlimitation, eczema, allergic eczema, flexural eczema, infantile eczema,nummular eczema, discoid lupus, prurigo Besnier, psoriasis, vitiligo,dermatitis, atopic dermatitis, perioral dermatitis, neurodermatitis,seborrheic dermatitis, rosacea, and acne.

Compositions and methods described herein may be used for the treatmentof atopic dermatitis. Treatment of the atopic dermatitis may result inreduced lesion size, reduced number of lesions, and/or a reduction inrelated symptoms. In addition, treatment of atopic dermatitis with acomposition or method described herein may reduce S. aureus in the skinof a subject in need thereof. Compositions and methods described hereinmay provide for enhanced barrier function of the skin as measured bytrans-epidermal water loss. Atopic dermatitis can occur as flare-ups,and there can be periods of remission. Administrations described herein,e.g., topical, oral, or rectal, may reduce reoccurrences, so thatadditional incidents of atopic dermatitis are reduced in number,intensity, or frequency. The administration may increase the time ofremission, such as the length of time between incidents. In someembodiments, an additional incident of atopic dermatitis does not occurfor 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 weeks followingapplication. In some embodiments, an additional incident of atopicdermatitis does not occur for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12months following the topical application.

Methods provided herein for treatment of a skin condition associatedwith dysbiosis may include measuring the microbiota of the skin of thesubject. Specifically, diagnostic assays can be performed to determinewhether the bacterial flora in the skin of a subject is alteredfollowing treatment compared to an original assessment. Alteration ofbacterial phyla, bacterial classes, bacterial orders, bacterialfamilies, bacterial genera, and/or bacterial species in the skin of asubject with atopic dermatitis can be determined. In some embodiments,the amount of S. aureus modified in the skin of the subject followingtreatment can be determined.

Such a method for identifying a microbiota in a sample can includeproviding a sample, such as a skin sample, and detecting at least onemicrobiota in the sample. In some embodiments, the method can includepreparing a nucleic acid sample including a molecular indicator ofidentity from at least one microbiota present in the sample anddetecting the molecular indicator of identity.

For example, the method can involve preparing at least one nucleic acidsample by preparing a DNA sample. The molecular indicator of identitycan be a polymorphic polynucleotide, such as an rRNA gene (for example,a 16S rRNA gene). The molecular indicator of identity can be detected bydetermining the nucleotide sequence of the polymorphic polynucleotide,such as the 16S rRNA gene, or a portion or subsequence thereof.Additional embodiments, for detecting the molecular indicator ofidentity can also include PCR with selective primers, quantitative PCRwith selective primers, DNA-DNA hybridization, RNA-DNA hybridization, insitu hybridization, and combinations thereof. For example, thepolymorphic polynucleotide can be detected by hybridization to aspecific probe. In such an example, the specific probe hybridizes to apolymorphic target nucleic acid, such as a 16S rRNA gene. Optionally,the nucleic acid can be hybridized to at least one array including aplurality of specific probes, e.g., a plurality of specific probes, eachof which identifies a species of bacteria. Detecting the molecularindicator of identity can also be accomplished using protein probes(such as antibodies) that bind to polymorphic target proteins, forexample, polymorphic target proteins that identify the microbiota.

The relative abundance of one or more bacteria, such as S. aureus, canbe measured in a sample from a subject. Relative abundance can refer tothe commonality or rarity of an organism relative to other organisms ina defined location or community. For example, the relative abundance canbe determined by generally measuring the presence of a particularorganism compared to the total presence of organisms in a sample.

The relative abundance of bacteria can be measured directly orindirectly. Direct measurements can include culture based methods.Indirect measurements can include comparing the prevalence of amolecular indicator of identity, such as ribosomal RNA (rRNA) genesequences, specific for an organism or group of organisms in relation tothe overall sample.

In some embodiments, the relative abundance of microbiota, such S.aureus and/or any type of bacteria, within the skin an individualsubject can be calculated by measuring the ratio of one or more specificbacteria in a sample from an individual to obtain a microbiota profileof the subject. The relative abundance can be derived from the totalabundance of bacteria present in a sample. The total abundance can referto the total bacteria in a sample. A microbiota profile can refer to arepresentation, such as a graph, of the relative abundance of one ormore microbiota in a subject or sample of skin from a subject.

Kits

Disclosed compositions can be provided as a component of a kit. Thepurified viable bacteria can be provided in a growth medium, lyophilizedform, or as frozen cells. Thus, the kit can include a containerincluding a therapeutically-effective amount of a purified viablebacteria and a metabolite.

In some embodiments, the kit can include the components needed toproduce a pharmaceutical composition, such as one container includingthe bacteria and one container including a pharmaceutically-acceptablecarrier for suspending the bacteria thereof. Thepharmaceutically-acceptable carrier can be, for example, a bufferedsaline solution or a sucrose solution. In other embodiments, the kit caninclude a container including the bacteria, and a second containerincluding a pharmaceutically-acceptable carrier, and a device, such as,but not limited to, a syringe, for measuring thepharmaceutically-acceptable carrier. In some embodiments, the kitincludes a device, such as, but not limited to, a spray nozzle or abandage, for topical application of the bacteria once it is suspended inthe pharmaceutically-acceptable carrier.

Optionally, such a kit includes additional components includingpackaging, instructions and various other reagents, such as additionalbuffers or other therapeutic ingredients. The kit can include acontainer and a label or package insert on or associated with thecontainer. Suitable containers can include, for example, bottles, vials,tubes, etc. The containers can be formed from a variety of materials,such as glass or plastic. The container can hold a composition includingbacteria effective for treating atopic dermatitis. In some embodiments,the container can have a sterile access port. For example, the containercan be an intravenous solution bag or a vial having a stopper pierceableby a hypodermic injection needle.

The label or package insert indicates that the composition can be usedfor treating the particular condition, such as atopic dermatitis. Thelabel or package insert typically will further include instructions foruse. The package insert typically includes instructions customarilyincluded in commercial packages of therapeutic products that containinformation about the indications, usage, dosage, administration,contraindications and/or warnings concerning the use of such therapeuticproducts. Non-limiting examples of instructions include information onthe amount of the pharmaceutically-acceptable carrier to add to the vialcontaining the bacteria, instructions for suspending the bacteria in thepharmaceutically-acceptable carrier, and instructions for topicalapplication to the skin. The application can be spraying on the skin,swabbing on the skin, or introducing the suspension onto a bandage forapplication to the skin.

The following examples are set forth to illustrate more clearly theprinciple and practice of embodiments disclosed herein to those skilledin the art and are not to be construed as limiting the scope of anyclaimed embodiments. Unless otherwise stated, all parts and percentagesare on a weight basis.

EXAMPLES Example 1: Oral Pharmaceutical Composition for Treatment ofStopic Dermatitis

A pharmaceutical composition is designed for treatment of atopicdermatitis including a strain of Roseomonas mucosa described herein inthe oral dosage form of a capsule.

Example 2: Rectal Pharmaceutical Composition for Treatment of AtopicDermatitis.

A pharmaceutical composition is designed for treatment of atopicdermatitis including a strain of Roseomonas mucosa described herein inthe rectal dosage form of a suppository.

Example 3: Combination Therapies in Mouse Model for Atopic Dermatitis

MC903, a vitamin D analogue, induces an AD-like dermatitis when appliedto mouse ears. For prevention studies, 1e7 CFU of gram negative bacteriais suspended in sterile PBS and dripped onto the mouse ears in 10 mcL ofvolume. Inoculations are initiated two days prior to MC903, andcontinued throughout the MC903 exposure. MC903 is placed first and theethanol was allowed to evaporate for 2 to 5 minutes prior to placementof bacterial isolates. Ear thickness is measured on day 14. Half themice are subject to co-inoculation of S. aureus, 1e6 CFU of the SAAS9strain of S. aureus which is dripped onto the ear immediately prior toinoculation with the gram negative isolate. Treatment studies areperformed by exposing mice to MC903 daily for 14 days and inoculatingwith 1e7 CFU total of strains provided in “Agent 1” (see Table 3) ondays 13 to 15. Agents 2 and 3 are also administered on days 13 to 15.Ear thickness is measured and photos taken on day 21. Serum total IgEanalysis: Serum was collected on day 14 of MC903. Serum is collected onday 14 of MC903 treatment and total IgE is determined. Bacterial strainsare donor derived, where the donor subject is a human donor not havingatopic dermatitis.

TABLE 3 Combination agent conditions. Route for Route for Route forCondition Agent 1 Agent 1 Agent 2 Agent 2 Agent 3 Agent 3 1 Roseomonasmucosa Topical None None 2 None Cyclosporine Topical None 3 None NoneDesonide Topical 4 None Cyclosporine Oral Desonide Topical 5 Roseomonasmucosa Topical Cyclosporine Oral None 6 Roseomonas mucosa TopicalCyclosporine Oral Desonide Topical 7 Roseomonas mucosa Topical NoneDesonide Topical 8 Pseudomonas Topical aeruginosa 9 Pseudomonas TopicalCyclosporine Oral None aeruginosa 10 Pseudomonas Topical CyclosporineOral Desonide Topical aeruginosa 11 Pseudomonas Topical None DesonideTopical aeruginosa 12 Roseomonas mucosa Topical None None andPseudomonas aeruginosa 13 Roseomonas mucosa Topical Cyclosporine OralNone and Pseudomonas aeruginosa 14 Roseomonas mucosa TopicalCyclosporine Oral Desonide Topical and Pseudomonas aeruginosa 15Roseomonas mucosa Topical None Desonide Topical and Pseudomonasaeruginosa 16 Staphylococcus Topical None None epidermis 17Staphylococcus Topical Cyclosporine Oral None epidermis 18Staphylococcus Topical Cyclosporine Oral Desonide Topical epidermis 19Staphylococcus Topical None Desonide Topical epidermis 20 StaphylococcusTopical None None epidermis and Roseomonas mucosa 21 StaphylococcusTopical Cyclosporine Oral None epidermis and Roseomonas mucosa 22Staphylococcus Topical Cyclosporine Oral Desonide Topical epidermis andRoseomonas mucosa 23 Staphylococcus Topical None Desonide Topicalepidermis and Roseomonas mucosa 24 Staphylococcus Topical None Nonehominis 25 Staphylococcus Topical Cyclosporine Oral None hominis 26Staphylococcus Topical Cyclosporine Oral Desonide Topical hominis 27Staphylococcus Topical None Desonide Topical hominis 28 StaphylococcusTopical None None hominis and Roseomonas mucosa 29 StaphylococcusTopical Cyclosporine Oral None hominis Roseomonas mucosa 30Staphylococcus Topical Cyclosporine Oral Desonide Topical hominisRoseomonas mucosa 31 Staphylococcus Topical None Desonide Topicalhominis Roseomonas mucosa 32 Staphylococcus Topical None None cohnii 33Staphylococcus Topical Cyclosporine Oral None cohnii 34 StaphylococcusTopical Cyclosporine Oral Desonide Topical cohnii 35 StaphylococcusTopical None Desonide Topical cohnii 36 Staphylococcus Topical None Nonecohnii Roseomonas mucosa 37 Staphylococcus Topical Cyclosporine OralNone cohnii Roseomonas mucosa 38 Staphylococcus Topical CyclosporineOral Desonide Topical cohnii Roseomonas mucosa 39 Staphylococcus TopicalNone Desonide Topical cohnii Roseomonas mucosa

Example 4: Treatment of Atopic Dermatitis Metabolite and a Microorganism

MC903, a vitamin D analogue, induces an AD-like dermatitis when appliedto mouse ears. For prevention studies, 1e7 CFU of gram negative bacteriais suspended in sterile PBS and dripped onto the mouse ears in 10mcL ofvolume. Inoculations are initiated two days prior to MC903, andcontinued throughout the MC903 exposure. MC903 is placed first, theethanol was allowed to evaporate for 2-5 minutes prior to placement ofbacterial isolates. Ear thickness is measured on day 14. Half the miceare subject to co-inoculation of S. aureus, 1e6 CFU of the SAAS9 strainof S. aureus which is dripped onto the ear immediately prior toinoculation with the gram negative isolate. Treatment studies isperformed by exposing mice to MC903 daily for 14 days and inoculatingwith 1e7 CFU total of Agent 1 (see Table 4) on days 13-15. Agent 2 isadministered on days 13-15. Ear thickness is measured and photos takenon day 21. Serum total IgE analysis: Serum was collected on day 14 ofMC903. Serum is collected on day 14 of MC903 treatment and total IgE isdetermined. Agent 2 can be any of the metabolites listed in Table 1.

TABLE 4 Combination agent regimens. Route for Route for Condition Agent1 Agent 1 Agent 2 Agent 2 1 Roseomonas mucosa Topical None 2 NonePhosphatidylcholine 37:2 Topical 3 Roseomonas mucosa TopicalPhosphatidylcholine 37:2 Topical 4 Pseudomonas aeruginosa Topical None 5Pseudomonas aeruginosa Topical Phosphatidylcholine 37:2 Topical 6Roseomonas mucosa and Topical None Topical Pseudomonas aeruginosa 7Roseomonas mucosa and Topical Phosphatidylcholine 37:2 TopicalPseudomonas aeruginosa 8 Staphylococcus epidermis Topical None 9Staphylococcus epidermis Topical Phosphatidylcholine 37:2 Topical 10Staphylococcus hominis Topical None 11 Staphylococcus hominis TopicalPhosphatidylcholine 37:2 Topical 12 Staphylococcus cohnii Topical None13 Staphylococcus cohnii Topical Phosphatidylcholine 37:2 Topical 14Propionibacterium acnes Topical None 15 Propionibacterium acnes TopicalPhosphatidylcholine 37:2 Topical 16 Moraxella osloensis Topical None 17Moraxella osloensis Topical Phosphatidylcholine 37:2 Topical 18Roseomonas mucosa and Topical None Pseudomonas aeruginosa 19 Roseomonasmucosa and Topical Phosphatidylcholine 37:2 Topical Pseudomonasaeruginosa 20 Roseomonas mucosa and Topical None Staphylococcusepidermis 21 Roseomonas mucosa and Topical Phosphatidylcholine 37:2Topical Staphylococcus epidermis 22 Roseomonas mucosa and Topical NoneStaphylococcus hominis 23 Roseomonas mucosa and TopicalPhosphatidylcholine 37:2 Topical Staphylococcus hominis 24 Roseomonasmucosa and Topical None Staphylococcus cohnii 25 Roseomonas mucosa andTopical Phosphatidylcholine 37:2 Topical Staphylococcus cohnii 26Roseomonas mucosa and Topical None Propionibacterium acnes 27 Roseomonasmucosa and Topical Phosphatidylcholine 37:2 Topical Propionibacteriumacnes 28 Roseomonas mucosa and Topical None Moraxella osloensis 29Roseomonas mucosa and Topical Phosphatidylcholine 37:2 Topical Moraxellaosloensis 30 Pseudomonas aeruginosa and Topical None Staphylococcusepidermis 31 Pseudomonas aeruginosa and Topical Phosphatidylcholine 37:2Topical Staphylococcus epidermis 32 Pseudomonas aeruginosa and TopicalNone Staphylococcus hominis 33 Pseudomonas aeruginosa and TopicalPhosphatidylcholine 37:2 Topical Staphylococcus hominis 34 Pseudomonasaeruginosa and Topical None Staphylococcus cohnii 35 Pseudomonasaeruginosa and Topical Phosphatidylcholine 37:2 Topical Staphylococcuscohnii 36 Pseudomonas aeruginosaand Topical None Propionibacterium acnes37 Pseudomonas aeruginosa and Topical Phosphatidylcholine 37:2 TopicalPropionibacterium acnes 38 Pseudomonas aeruginosa and Topical NoneMoraxella osloensis 39 Pseudomonas aeruginosa and TopicalPhosphatidylcholine 37:2 Topical Moraxella osloensis 40 Moraxellaosloensis and Topical None Staphylococcus epidermis 41 Moraxellaosloensis and Topical Phosphatidylcholine 37:2 Topical Staphylococcusepidermis 42 Moraxella osloensis and Topical None Staphylococcus hominis43 Moraxella osloensis and Topical Phosphatidylcholine 37:2 TopicalStaphylococcus hominis 44 Moraxella osloensis and Topical NoneStaphylococcus cohnii 45 Moraxella osloensis and TopicalPhosphatidylcholine 37:2 Topical Staphylococcus cohnii 46 Moraxellaosloensis and Topical None Propionibacterium acnes 47 Moraxellaosloensis and Topical Phosphatidylcholine 37:2 Topical Propionibacteriumacnes

Example 5: Treatment of Atopic Dermatitis with Metabolite and AdditionalTherapeutic Agents

MC903, a vitamin D analogue, induces an AD-like dermatitis when appliedto mouse ears. For prevention studies, 1e7 CFU of gram negative bacteriais suspended in sterile PBS and dripped onto the mouse ears in 10 mcL ofvolume. Inoculations are initiated two days prior to MC903, andcontinued throughout the MC903 exposure. MC903 is placed first, theethanol was allowed to evaporate for 2-5 minutes prior to placement ofbacterial isolates. Ear thickness is measured on day 14. Half the miceare subject to co-inoculation of S. aureus, 1e6 CFU of the SAAS9 strainof S. aureus which is dripped onto the ear immediately prior toinoculation with the gram negative isolate. Treatment studies isperformed by exposing mice to MC903 daily for 14 days and inoculatingwith 1e7 CFU total of Agent 1 (see Table 5) on days 13-15. Agents 2 and3 are administered on days 13-15. Ear thickness is measured and photostaken on day 21. Serum total IgE analysis: Serum was collected on day 14of MC903. Serum is collected on day 14 of MC903 treatment and total IgEis determined.

TABLE 5 Combination therapy regimen. Route for Route for Route forSubject Agent 1 Agent 1 Agent 2 Agent 2 Agent 3 Agent 3 1 Roseomonasmucosa Topical None None 2 None Desonide Topical None 3 None NonePhosphatidylcholine 37:2 Topical 4 Roseomonas mucosa Topical DesonideTopical None 5 Roseomonas mucosa Topical None Phosphatidylcholine 37:2Topical 6 None Desonide Topical Phosphatidylcholine 37:2 Topical 7Roseomonas mucosa Topical Desonide Topical Phosphatidylcholine 37:2Topical 8 Pseudomonas Topical None None aeruginosa 9 Pseudomonas TopicalDesonide Topical None aeruginosa 10 Pseudomonas Topical Desonide TopicalPhosphatidylcholine 37:2 Topical aeruginosa 11 Pseudomonas Topical NonePhosphatidylcholine 37:2 Topical aeruginosa 12 Roseomonas mucosa TopicalNone None and Pseudomonas aeruginosa 13 Roseomonas mucosa TopicalDesonide Topical None and Pseudomonas aeruginosa 14 Roseomonas mucosaTopical Desonide Topical Phosphatidylcholine 37:2 Topical andPseudomonas aeruginosa 15 Roseomonas mucosa Topical NonePhosphatidylcholine 37:2 Topical and Pseudomonas aeruginosa 16Staphylococcus Topical None None epidermis 17 Staphylococcus TopicalCyclosporine Oral None epidermis 18 Staphylococcus Topical CyclosporineOral Desonide Topical epidermis 19 Staphylococcus Topical None DesonideTopical epidermis 20 Staphylococcus Topical None None epidermisRoseomonas mucosa 21 Staphylococcus Topical Cyclosporine Oral Noneepidermis Roseomonas mucosa 22 Staphylococcus Topical Cyclosporine OralDesonide Topical epidermis Roseomonas mucosa 23 Staphylococcus TopicalNone Desonide Topical epidermis Roseomonas mucosa 24 StaphylococcusTopical None None hominis 25 Staphylococcus Topical Cyclosporine OralNone hominis 26 Staphylococcus Topical Cyclosporine Oral DesonideTopical hominis 27 Staphylococcus Topical None Desonide Topical hominis28 Staphylococcus Topical None None hominis Roseomonas mucosa 29Staphylococcus Topical Cyclosporine Oral None hominis Roseomonas mucosa30 Staphylococcus Topical Cyclosporine Oral Desonide Topical hominisRoseomonas mucosa 31 Staphylococcus Topical None Desonide Topicalhominis Roseomonas mucosa 32 Staphylococcus Topical None None cohnii 33Staphylococcus Topical Cyclosporine Oral None cohnii 34 StaphylococcusTopical Cyclosporine Oral Desonide Topical cohnii 35 StaphylococcusTopical None Desonide Topical cohnii 36 Staphylococcus Topical None Nonecohnii Roseomonas mucosa 37 Staphylococcus Topical Cyclosporine OralNone cohnii Roseomonas mucosa 38 Staphylococcus Topical CyclosporineOral Desonide Topical cohnii Roseomonas mucosa 39 Staphylococcus TopicalNone Desonide Topical cohnii Roseomonas mucosa

Example 6: Culturing Gram Negative Bacteria from Healthy Donors to AssesS. aureus Growth Inhibition

Overgrowth and infection with S. aureus is both a contributor to, andconsequence of, the immune imbalance and poor barrier functioncharacteristic of atopic dermatitis. Multiple isolates of S. aureus aregrown in the presence of the supernatant from cultures of healthy donor(HV)-derived bacteria or bacteria derived from a skin lesion of asubject having atopic dermatitis, eczema, allergic eczema, flexuraleczema, infantile eczema, nummular eczema, discoid lupus, prurigoBesnier, psoriasis, vitiligo, dermatitis, atopic dermatitis, perioraldermatitis, neurodermatitis, seborrheic dermatitis, rosacea, or acne. S.aureus growth is assessed.

Co-inoculation of the cultured HV-derived bacteria or bacteria derivedfrom a subject having a disease associated with skin dysbiosis with S.aureus are contacted to mouse ears and S. aureus yields are recorded.Lipid metabolite level for lysophosphatidylcholine (LPC) is alsoassessed. HV-derived bacteria referenced in Table 6 are assessed.

TABLE 6 Conditions. Condition Agents 1 Saline 2 Roseomonas mucosa 3Pseudomonas aeruginosa 4 Staphylococcus epidermis 5 Staphylococcushominis 6 Staphylococcus cohnii 7 Propionibacterium acnes 8 Moraxellaosloensis 9 Roseomonas mucosa, Pseudomonas aeruginosa 10 Roseomonasmucosa, Staphylococcus epidermis 11 Roseomonas mucosa, Staphylococcushominis 12 Roseomonas mucosa, Staphylococcus cohnii 13 Roseomonasmucosa, Propionibacterium acnes 14 Roseomonas mucosa, Moraxellaosloensis 15 Pseudomonas aeruginosa, Staphylococcus epidermis 16Pseudomonas aeruginosa, Staphylococcus hominis 17 Pseudomonasaeruginosa, Staphylococcus cohnii 18 Pseudomonas aeruginosa,Propionibacterium acnes 19 Pseudomonas aeruginosa, Moraxella osloensis20 Moraxella osloensis, Staphylococcus epidermis 21 Moraxella osloensis,Staphylococcus hominis 22 Moraxella osloensis, Staphylococcus cohnii 23Moraxella osloensis, Propionibacterium acnes

Example 7: Culturing Gram Negative Bacteria from Healthy Donors toInduce Innate Immunity in Humans

To measure in vivo human cutaneous immune reactivity to bacteriadescribed herein, human foreskin-derived primary keratinocytes (KC) areinfected with isolates of live healthy donor-derived bacteria orbacteria derived from a skin lesion of a subject having atopicdermatitis, eczema, allergic eczema, flexural eczema, infantile eczema,nummular eczema, discoid lupus, prurigo Besnier, psoriasis, vitiligo,dermatitis, atopic dermatitis, perioral dermatitis, neurodermatitis,seborrheic dermatitis, rosacea, or acne. 20-24 hours after infection,KCs exposed to HV-bacteria are screened for a relative increase comparedto those exposed to bacteria derived from the subject having the diseaseassociated with skin dysbiosis for increase in mRNA levels for defensinβ4A, CYP27b1 (a vitamin D converting enzyme), the vitamin D receptor(VDR), and the anti-microbial peptide cathelicidin. HV-derived bacteriareferenced in Table 3 are assessed.

Example 8: Culturing Gram Negative Bacteria from Healthy Donors toAssess Barrier Function in Mice

The loss of barrier function in AD causes dry, itchy skin due totrans-epidermal water loss (TEWL) and cutaneous sensitization toantigens. For a subset of subjects, this barrier defect is associatedwith dysfunction in the tight-junction protein filaggrin. Isolates oflive HV-derived bacteria or bacteria derived from a skin lesion of asubject having atopic dermatitis are topically applied to healthy mouseears, which are subsequently assessed for enhanced transcript levels offilaggrin, ear thickness change, and TWEL. HV-derived bacteriareferenced in Table 3 are assessed. Combination agent delivery asdescribed in Table 5 is also assessed.

Example 9: Culturing Gram Negative Bacteria from Healthy Donors toAssess Outcomes in a Mouse Model of Atopic Dermatitis

MC903, a vitamin D analogue, induces an AD-like dermatitis when appliedto mouse ears. Isolates of live HV-derived bacteria or bacteria derivedfrom a subject having atopic dermatitis are topically applied to healthymouse ears prior to administration of MC903. Ear thickness, serum IgEinduction, mRNA levels (for filaggrin, defensin β4A, CYP27b1, VDR, andcathelicidin), are compared before and after MC903 administration.HV-derived bacteria referenced in Table 3 are assessed. Combinationagent delivery as described in Table 5 is also assessed.

Example 10: Generation and Characterization of a PharmaceuticalFormulation of R. mucosa from Healthy Volunteers

Three isolates of R. mucosa from 3 human healthy volunteers (HVs) aregrown in minimal media (R2A broth, Teknova; or Hanks Buffered SaltSolution, HBSS, Gibco) for 24-48 hours. Isolates are selected based ontheir ability to inhibit the growth of S. aureus, activate vitamin Dpathways in human keratinocytes, and improve outcomes in mouse models ofAD. The isolates are referenced as RM-A, RM-B, and RM-C. Genomicsequencing is performed on all strains to verify that no transmittable,clinically significant antibiotic resistance genes were present. Thebacterial cells are washed 3 times in PBS (Gibco) and resuspended into10%-15% sucrose in water for a concentration of 109 CFU/ml. Serialdilutions are performed in 10%-15% sucrose to generate stocks of 104,105, and 106 per ml. Aliquots of diluted bacterial samples are plated onR2A agar (Remel) and incubated at 32° C. for 48-72 hours to enumerateprelyophilization CFU concentration. Eight hundred microliters (adult)or 1.5 ml (pediatric) of bacterial solution is frozen in 1.5-ml amberglass vials (Wheaton; adult) or a 3-ml self-contained sprayer system(Discount Vials; pediatrics) prior to lyophilization (Labconco).Vials/sprayers are sealed, labeled, and stored at −70° C. untildispensed to the patients.

Genomes from the three isolates of R. mucosa have regions of sequencespecific to each of the three isolates, as show in in Table 7 (basesspecific to each strain are in bold and underlined).

TABLE 7 SEQ ID Strain Nucleic Acid NO: RM-A CGGCGGCGGACAGCCCCTCCAC C CC1 A TCCTCGCCGAGCCCGATGATGCTAA RM-B CGGCGGCGGACAGCCCCTCCAC T CC 2 ACCTCGCCGAGCCCGATGATGCTAA RM-C CGGCGGCGGACAGCCCCTCCAC C CC 3 GTCCTCGCCGAGCCCGATGATGCTAA

Primers designed to amplify the region where strain specific variationis identified. A Custom TaqMan® SNP Genotyping Assays, Non-human, SM kitand protocol is used to perform an analysis for detection of eachstrain. Briefly, DNA from each isolate is subjected to PCR where theprimers were SEQ ID NO: 4 (CACCGGACAGCAGGCT), and SEQ ID NO: 5(GCGGTGGCTTAGCATCATC). Amplification products are subjected to anallelic discrimination assay. In a first comparison, the followingreporters are used: SEQ ID NO: 6 (CACCCCATCCTCG) and SEQ ID NO: 7(CACCCCGTCCTCG). This is an A/G allelic discrimination assay. In asecond comparison, the following reporters are used: SEQ ID NO: 8(CCCTCCACCCCATCCT) and SEQ ID NO: 9 (CCCTCCACTCCATCCT). This is a T/Callelic discrimination assay.

Example 11: MC903-Induced Atopic Dermatitis Model in Mice.

Balb/c male mice are subject to a model for induction of atopicdermatitis. MC903 is dissolved in 100% ethanol and topically applied onmouse ears (2 and 4 nmol in 25 μl per ear) for 14 days. A control groupis treated with ethanol only. Gradual induction of lesions in the ear inmice is monitored by scoring for ear thickness, appearance of scars andredness. Every other day in-life observations are done from Day 5 to Day15, and ears are collected on Day 15 for histo-pathological evaluationof the disease. The route of administration is oral gavage, twice daily.Subjects are divided as summarized below in Table 8.

TABLE 8 Dose Population Group (mg/kg) N 1. Control Naive (optional) 0 102. Vehicle 0 10 3. MC903, Dose 1 TBD 10 4. MC903, Dose 2 TBD 10 5.MC903, Dose 1 + 62.5 mg/day 10 Positive control (Clobetasol cream,0.05%) 6. Positive control 62.5 mg/day 10 (Clobetasol cream, 0.05%)

The acclimation period before start of treatment is at least five days.Body weight is measured before start of model induction and then beforeeach dosing. Baseline thickness of the ear is taken by digital caliperand animals are randomized into different treatment groups. From Day 5to Day 15, assessment of ear thickness, erythema score and skin scalingscore are done. On Day 15, the right ear is collected from all animals,and fixed in 10% NBF for histopathological assessment. The left ear iscollected and snap frozen for future gene or cytokine analysis. Spleenand lymph nodes are also collected. Terminal serum is collected and keptfor potential IgE antibody analysis. H&E staining of right ears (oneslide/animal) is performed, histological evaluation of Epidermalthickness is performed using the Image-Pro system. Subjects are dosedwith single and combination therapies as described in Example 3, Table3.

Example 12: Imiquimod (IMQ)-Induced Psoriasis Model in Mice

Balb-c male mice are subject to a model for psoriasis. Animals receive62.5 mg of 5% IMQ cream topically on the back skin (we can perform thismodel using ears if there is limitation for test item availability) oncedaily from Day 1 to Day 11. IMQ causes gradual induction ofpsoriasis-like lesions in the skin in mice as evidenced by increase inthickness, appearance of scars and redness. Daily in-life observationsare done from Day 2 to Day 12, and back skin is collected on Day 12 forpossible histopathological evaluation of the disease. Dosing regimen isto start 3 days prior to first IMQ application on Day-3. Administrationis daily by topical administration. Subjects are divided as summarizedbelow in Table 9.

TABLE 9 Dose Population Group (mg/kg) N Test System: 1. Control Naive(optional) 0 10 2. IMQ + Vehicle 0 10 3. IMQ + TI, 1 TBD 10 4. IMQ + TI,2 TBD 10 5. IMQ + Positive control 62.5 mg/day 10 (Clobetasol cream,0.05%)

Subjects are given an acclimation period of at least 5 days beforeinitiation of treatment. Body weight is measured once before start ofIMQ application and then before each dosing. On Day 0, baselinethickness of the back skin is taken by a digital caliper and animals arerandomized into different treatment groups. From Day 2 to Day 12, dailyassessment of back skin thickness, skin erythema score and skin scalingscore are done. Skin samples collected from all animals at terminationand analysis for IL13, TNFa, MIP-1a, G-CSF and IL-17 (5plex) using aBio-Rad kit. Terminal Procedures: On Day 12, back skin is collected fromall animals, and fixed in 10% NBF for histopathological assessment. Ifrequired, skin samples are snap frozen for cytokine analysis. Terminalblood plasma/serum is collected. H&E staining of back skin and/or earsections is performed (one slide/animal). Epidermal thickness,Parakeratosis, Acanthosis and Inflammatory infiltrate scorings, and aComposite score are performed. Subjects are dosed with single andcombination therapies as described in Example 3, Table 3.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby.

What is claimed is:
 1. A method for treatment of a skin conditionassociated with inflammation or barrier disruption, comprisingadministering to a subject in need thereof: a. a metabolite; and b. atleast one strain of a live, purified gram-negative bacteria, wherein theadministering provides for reduction of a skin condition associated withinflammation or barrier disruption in the subject.
 2. The method ofclaim 1, wherein the metabolite is N4-acetylaminobutanal,5-ethylpentadecane-2,4-dione, ricinoleic acid methyl ester, trenboloneacetate, or N-(2-hydroxyethyl)-11(12)-epoxy-5Z,8Z,14Z-eicosatrienamide.3. The method of claim 1, wherein the metabolite is a lipid.
 4. Themethod of claim 3, wherein the lipid is at least onephosphatidylethanolamine.
 5. The method of claim 3, wherein the lipidcomprises phosphatidylethanolamine 36:2, phosphatidylcholine 37:0,phosphatidylcholine 37:2, phosphatidylcholine 38:2,phosphatidylcholine(18:2(9Z,12Z)/18:0), phosphatidylethanolamine14:0/20:1, phosphatidylethanolamine 22:1/14:1, or 8-keto palmitic acid.6. The method of claim 1, wherein the metabolite is a peptide.
 7. Themethod of claim 6, wherein the peptide comprises Tyr-Leu-Arg.
 8. Themethod of claim 1, wherein the metabolite is a sugar.
 9. The method ofclaim 8, wherein the sugar comprises maltopentaose.
 10. The method ofclaim 1, wherein the metabolite is a nucleotide.
 11. The method of claim10, wherein the nucleotide comprises 2′-deoxyguanosine 5′-monophosphate.12. The method of claim 1, wherein the metabolite is in a topical dosageform.
 13. The method of claim 12, wherein the topical dosage form is aliquid, cream, gel, or foam.
 14. The method of claim 1, wherein thelive, purified gram negative bacteria comprises a species is of thegenus Pseudomonas, Pantoea, Moraxella, Roseomonas, or Vitreoscilla. 15.The method of claim 1, wherein the live, purified gram negative bacteriacomprises Roseomonas mucosa, Pseudomonas aeruginosa, or Moraxellaosloensis.
 16. The method of claim 1, wherein the live, purified gramnegative bacteria is Roseomonas mucosa.
 17. The method of claim 1,wherein the live, purified gram negative bacteria is in a topical dosageform.
 18. The method of claim 17, wherein the topical dosage form is aliquid, cream, gel, or foam.
 19. The method of claim 1, wherein themetabolite and the live, purified gram negative bacteria areconcurrently administered.
 20. The method of claim 1, wherein themetabolite and the live, purified gram negative bacteria are presenttogether in a pharmaceutical composition.
 21. The method of claim 1,wherein the metabolite and the live, purified gram negative bacteria arepresent in separate pharmaceutical compositions.
 22. The method of claim1, wherein the skin condition associated with inflammation or barrierdisruption is eczema, allergic eczema, flexural eczema, infantileeczema, nummular eczema, discoid lupus, prurigo Besnier, psoriasis,vitiligo, dermatitis, atopic dermatitis, perioral dermatitis,neurodermatitis, seborrheic dermatitis, rosacea, or acne.